Remove declarative api from chemistry

Author: manoelmarques

chemistry/README.md

@@ -4,15 +4,4 @@ This folder contains some Jupyter Notebook examples showing how to run chemistry
 Qiskit Chemistry. There are also Python code files too as well as some hdf5 files containing saved
 molecular data that may be used in experiments.
 
-These example programs and notebooks show how to use the dictionary equivalent form of
-the [input file](#input-files) that can be used more effectively programmatically when your goal is to
-run the content with a range of different values. For example the [energyplot](energyplot.ipynb) notebook
-alters the interatomic distance of a molecule, over a range of values, and uses the results to plot graphs.
-
 For more detail see the main [index](../index.ipynb#chemistry)
-
-## Input files
-
-The folder [input_files](input_files) contains a number of example input files that can be loaded
-and run by the Qiskit Chemistry [GUI](https://github.com/Qiskit/qiskit-chemistry/blob/master/README.md#gui) or by the
-[command line](https://github.com/Qiskit/qiskit-chemistry/blob/master/README.md#command-line) tool.

chemistry/beh2_reductions.ipynb

@@ -10,8 +10,6 @@
     "\n",
     "This notebook demonstrates this for Beryllium Dihydride (BeH2) where we show the effect of removing different unoccupied orbitals. We use Qiskit Chemistry to plot graphs of the ground state energy of the Beryllium Dihydride (BeH2) molecule over a range of inter-atomic distances using ExactEigensolver. Freeze core reduction is true and different virtual orbital removals are tried as a comparison.\n",
     "\n",
-    "This notebook populates a dictionary, that is a progammatic representation of an input file, in order to drive the Qiskit Chemistry stack. Such a dictionary can be manipulated programmatically and this is indeed the case here where we alter the molecule supplied to the driver in each loop as well as the orbital reductions.\n",
-    "\n",
     "This notebook has been written to use the PYSCF chemistry driver."
    ]
   },
@@ -102,7 +100,6 @@
     "        qubit_op, aux_ops = operator.run(qmolecule)\n",
     "        result = ExactEigensolver(qubit_op).run()\n",
     "        lines, result = operator.process_algorithm_result(result)\n",
-    "        result['printable'] = lines\n",
     "        energies[j][i] = result['energy']\n",
     "    distances[i] = d\n",
     "print(' --- complete')\n",
@@ -318,7 +315,6 @@
     "    qubit_op, aux_ops = operator.run(qmolecule)\n",
     "    result = ExactEigensolver(qubit_op).run()\n",
     "    lines, result = operator.process_algorithm_result(result)\n",
-    "    result['printable'] = lines\n",
     "    e_nofreeze[i] = result['energy']\n",
     "\n",
     "print(e_nofreeze)"

chemistry/dictinput.py

@@ -20,8 +20,8 @@
 from qiskit.chemistry.core import Hamiltonian
 
 
-# An example of using a loop to vary inter-atomic distance. A dictionary is
-# created outside the loop, but inside the loop the 'atom' value is updated
+# An example of using a loop to vary inter-atomic distance.
+# Inside the loop the 'atom' value is updated
 # with a new molecular configuration. The molecule is H2 and its inter-atomic distance
 # i.e the distance between the two atoms, is altered from 0.5 to 1.0. Each atom is
 # specified by x, y, z coords and the atoms are set on the z-axis, equidistant from

chemistry/energyplot.ipynb

@@ -10,8 +10,6 @@
     "\n",
     "This notebook demonstrates using Qiskit Chemistry to plot graphs of the ground state and excited state energies of the Hydrogen (H2) molecule over a range of inter-atomic distances. This notebook utilizes the fact that when two_qubit_reduction is used with the parity mapping on H2 the resultant hamiltionian solely contains the 4 states we are looking for.\n",
     "\n",
-    "This notebook populates a dictionary, that is a progammatic representation of an input file, in order to drive the Qiskit Chemistry stack. Such a dictionary can be manipulated programmatically and this is indeed the case here where we alter the molecule supplied to the driver in each loop.\n",
-    "\n",
     "This notebook has been written to use the PYSCF chemistry driver."
    ]
   },
@@ -73,8 +71,7 @@
     "    qubit_op, aux_ops = operator.run(qmolecule)\n",
     "    result = ExactEigensolver(qubit_op, k=4).run()\n",
     "    lines, result = operator.process_algorithm_result(result)\n",
-    "    result['printable'] = lines\n",
-    "\n",
+    "   \n",
     "    energies[:, i] = result['energies']\n",
     "    distances[i] = d\n",
     "print(' --- complete')\n",

chemistry/h2_basis_sets.ipynb

@@ -10,8 +10,6 @@
     "\n",
     "This notebook demonstrates using Qiskit Chemistry to plot graphs of the ground state energy of the Hydrogen (H2) molecule over a range of inter-atomic distances with different fermionic mappings to quantum qubits.\n",
     "\n",
-    "This notebook populates a dictionary, that is a progammatic representation of an input file, in order to drive the Qiskit Chemistry stack. Such a dictionary can be manipulated programmatically and this is indeed the case here where we alter the molecule supplied to the driver in each loop.\n",
-    "\n",
     "This notebook has been written to use the PYSCF chemistry driver."
    ]
   },
@@ -79,14 +77,6 @@
     "from qiskit.chemistry.drivers import PySCFDriver\n",
     "from qiskit.chemistry.core import Hamiltonian, QubitMappingType\n",
     "\n",
-    "# Input dictionary to configure Qiskit Chemistry for the chemistry problem.\n",
-    "qiskit_chemistry_dict = {\n",
-    "    'problem': {'random_seed': 50},\n",
-    "    'driver': {'name': 'PYSCF'},\n",
-    "    'PYSCF': {'atom': '', 'basis': 'sto3g'},\n",
-    "    'operator': {'name': 'hamiltonian', 'qubit_mapping': '', 'two_qubit_reduction': False},\n",
-    "    'algorithm': {'name': ''}\n",
-    "}\n",
     "molecule = 'H .0 .0 -{0}; H .0 .0 {0}'\n",
     "\n",
     "algorithms = ['VQE', 'ExactEigensolver']\n",
@@ -107,15 +97,6 @@
     "    print('\\b\\b{:2d}'.format(i), end='', flush=True)\n",
     "    d = start + i*by/steps \n",
     "    for j in range(len(algorithms)):\n",
-    "        if algorithms[j] == 'ExactEigensolver':\n",
-    "            if 'optimizer' in qiskit_chemistry_dict:\n",
-    "                del qiskit_chemistry_dict['optimizer']\n",
-    "            if 'variational_form' in qiskit_chemistry_dict:\n",
-    "                del qiskit_chemistry_dict['variational_form']\n",
-    "        else:\n",
-    "            qiskit_chemistry_dict['optimizer'] = {'name': 'L_BFGS_B', 'maxfun': 2500}\n",
-    "            qiskit_chemistry_dict['variational_form'] = {'name': 'RYRZ', 'depth': 5}\n",
-    "        \n",
     "        for k in range(len(mappings)): \n",
     "            driver = PySCFDriver(molecule.format(d/2), basis='sto3g')\n",
     "            qmolecule = driver.run()\n",
@@ -132,7 +113,6 @@
     "                                    seed_transpiler=aqua_globals.random_seed))\n",
     "\n",
     "            lines, result = operator.process_algorithm_result(result)\n",
-    "            result['printable'] = lines\n",
     "            energies[k][j][i] = result['energy']\n",
     "            hf_energies[i] = result['hf_energy']  # Independent of algorithm & mapping\n",
     "    distances[i] = d\n",

chemistry/h2_excited_states.ipynb

@@ -118,7 +118,6 @@
     "                                    seed_transpiler=aqua_globals.random_seed))\n",
     "        \n",
     "            lines, result = operator.process_algorithm_result(result)\n",
-    "            result['printable'] = lines\n",
     "            energies[k][j][i] = result['energy']\n",
     "            hf_energies[i] = result['hf_energy']\n",
     "            if algorithms[j] == 'VQE':\n",

chemistry/h2_mappings.ipynb

@@ -96,7 +96,6 @@
     "                                seed_transpiler=aqua_globals.random_seed))\n",
     "        \n",
     "        lines, result = operator.process_algorithm_result(result)\n",
-    "        result['printable'] = lines\n",
     "        energies[j][i] = result['energy']\n",
     "        hf_energies[i] = result['hf_energy']\n",
     "        if algorithms[j] == 'VQE':\n",

chemistry/h2_particle_hole.ipynb

@@ -8,8 +8,6 @@
     "\n",
     "This notebook demonstrates using Qiskit Chemistry to plot graphs of the ground state energy of the Hydrogen (H2) molecule over a range of inter-atomic distances using VQE and UCCSD. It is compared to the same energies as computed by the ExactEigensolver. `UCCSD` should be used together with `HartreeFock` initial state.\n",
     "\n",
-    "This notebook populates a dictionary, that is a progammatic representation of an input file, in order to drive the Qiskit Chemistry stack. Such a dictionary can be manipulated programmatically and this is indeed the case here where we alter the molecule supplied to the driver in each loop.\n",
-    "\n",
     "This notebook has been written to use the PYQUANTE chemistry driver. See the PYQUANTE chemistry driver readme if you need to install the external PyQuante2 library that this driver requires."
    ]
   },
@@ -100,7 +98,6 @@
     "            result = algo.run(QuantumInstance(BasicAer.get_backend('statevector_simulator')))\n",
     "        \n",
     "        lines, result = operator.process_algorithm_result(result)\n",
-    "        result['printable'] = lines\n",
     "        energies[j][i] = result['energy']\n",
     "        hf_energies[i] = result['hf_energy']\n",
     "        if algorithms[j] == 'VQE':\n",