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Models module (#51)
* creating hamiltonian module * before testing * tests passing * all tests passing * fixed docs * docker readme, version number * addressed Jarrod's comments * minor change to readme * changed ops init
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‎README.rst‎

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@@ -34,7 +34,7 @@ as well as our detailed `code documentation <http://openfermion.readthedocs.io/e
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Developer install
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-----------------
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To install the latest version of OpenFermion in development mode:
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To install the latest version of OpenFermion (in development mode):
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.. code-block:: bash
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‎docker/README.md‎

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@@ -105,7 +105,7 @@ necessary applications needed for running these programs. To run the image, use
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and the terminal enters a new environment which emulates a Ubuntu OS with
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OpenFermion and accessories installed, regardless of what the host OS is. This
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new environment is a running process called a Docker container. To check info
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on the container, one can open another terminal, configure it using
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on the container, one can open another terminal, configure it using
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`docker-machine env` as mentioned before, and run
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```
@@ -135,12 +135,11 @@ container, run in a separate terminal from the one running the container
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where container name can be gleaned according to the step above.
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An alternative way of loading files onto the Docker container is through
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remote repos such as Github or BitBucket. git is installed in the Docker image.
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remote repos such as Github or BitBucket. git is installed in the Docker image.
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After `docker run`, one could run "git clone ..." etc to pull files
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remotely into the Docker container.
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There are occasions where one might want to open up multiple terminals to
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run the same Docker container. In that case, one could run in any terminal
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remotely into the Docker container. There are occasions where one might want
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to open up multiple terminals to run the same Docker container.
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In that case, one could run in any terminal
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```
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docker exec -it [container name] bash
@@ -160,7 +159,7 @@ backend, first check the ip address of the virtual machine by running
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where "default" can be replaced by the name of whichever virtual machine whose
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ip address you want to check.
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Assuming the Docker image for OpenFermion is already built and is called
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Assuming the Docker image for OpenFermion is already built and is called
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openfermion_docker, run the container with an additional -p flag:
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@@ -179,7 +178,7 @@ When the terminal enters the Docker container, run Jupyter notebook by
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```
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where 8888 is the port number used previously for setting up the container.
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The message returned to the terminal should end with a statement that says
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The message returned to the terminal should end with a statement that says
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something like:
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```
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Copy/paste this URL into your browser when you connect for the first time,
@@ -188,7 +187,7 @@ to login with a token:
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```
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Note the token string 8f70c035fb9b0dbbf160d996f7f341fecf94c9aedc7cfaf7.
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Open a browser window and type in the address line
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Open a browser and type in the address line
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```
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[virtual machine ip]:8888
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where [virtual machine ip] is extracted from `docker-machine ip` and 8888 is the port
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number (or any other port number that one specifies previously). A webpage
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asking for token string should appear. Use the token string obtained from before to
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enter Jupyter Notebook. If logged in successfully, you should be able to freely
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enter Jupyter Notebook. If logged in successfully, you should be able to freely
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navigate through the entire Docker image and launch any Jupyter notebook in the image.

‎docs/examples.rst‎

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@@ -135,12 +135,13 @@ We see that despite the different representation, these operators are iso-spectr
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Sparse matrices and the Hubbard model
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-------------------------------------
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Often, one would like to obtain a sparse matrix representation of an operator which can be analyzed numerically. There is code in both openfermion.transforms and openfermion.utils which facilitates this. The function get_sparse_operator converts either a FermionOperator, a QubitOperator or other more advanced classes such as InteractionOperator to a scipy.sparse.csc matrix. There are numerous functions in openfermion.utils which one can call on the sparse operators such as "get_gap", "get_hartree_fock_state", "get_ground_state", ect. We show this off by computing the ground state energy of the Hubbard model. To do that, we use code from the openfermion.utils module which constructs lattice models of fermions such as Hubbard models.
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Often, one would like to obtain a sparse matrix representation of an operator which can be analyzed numerically. There is code in both openfermion.transforms and openfermion.utils which facilitates this. The function get_sparse_operator converts either a FermionOperator, a QubitOperator or other more advanced classes such as InteractionOperator to a scipy.sparse.csc matrix. There are numerous functions in openfermion.utils which one can call on the sparse operators such as "get_gap", "get_hartree_fock_state", "get_ground_state", ect. We show this off by computing the ground state energy of the Hubbard model. To do that, we use code from the openfermion.hamiltonians module which constructs lattice models of fermions such as Hubbard models.
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.. code-block:: python
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from openfermion.hamiltonians import fermi_hubbard
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from openfermion.transforms import get_sparse_operator, jordan_wigner
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from openfermion.utils import fermi_hubbard, get_ground_state
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from openfermion.utils import get_ground_state
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# Set model.
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x_dimension = 2
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.. code-block:: python
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from openfermion.utils import MolecularData
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from openfermion.hamiltonians import MolecularData
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# Set parameters to make a simple molecule.
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diatomic_bond_length = .7414
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.. code-block:: python
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from openfermion.hamiltonians import MolecularData
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from openfermion.transforms import get_fermion_operator, get_sparse_operator, jordan_wigner
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from openfermion.utils import get_ground_state, MolecularData
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from openfermion.utils import get_ground_state
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import numpy
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import scipy
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import scipy.linalg

‎docs/index.rst‎

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===================
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Contents
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* :ref:`intro`: Introduction & Installation
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* :ref:`examples`: Code examples
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* :ref:`codedoc`: The code documentation of openfermion.
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* :ref:`intro`: Introduction & Installation
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* :ref:`examples`: Code examples
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* :ref:`codedoc`: The code documentation of openfermion.
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.. toctree::
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:maxdepth: 2
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:hidden:
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:maxdepth: 2
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:hidden:
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intro
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examples
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openfermion
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intro
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examples
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openfermion
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‎docs/openfermion.rst‎

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Code Documentation
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==================
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openfermion.hamiltonians
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--------------
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.. automodule:: openfermion.hamiltonians
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:members:
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:special-members: __init__
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:imported-members:
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openfermion.measurements
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--------------
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‎examples/givens_rotations.ipynb‎

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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[[-0.311+0.062j -0.403-0.276j 0.097-0.412j 0.237-0.295j 0.091-0.504j 0.236-0.145j]\n",
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" [-0.289-0.156j -0.113+0.033j 0.262+0.525j -0.207+0.253j -0.212-0.122j 0.365-0.484j]\n",
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" [-0.330-0.72j -0.018-0.099j -0.236-0.182j -0.185+0.005j -0.015+0.025j -0.460-0.164j]]\n"
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"[[-0.134+0.446j 0.018+0.271j 0.703+0.294j 0.025-0.198j -0.074+0.061j 0.267-0.091j]\n",
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" [ 0.336+0.267j -0.441-0.245j -0.077-0.02j 0.343+0.422j 0.083+0.215j 0.434-0.131j]\n",
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" [-0.395-0.103j 0.001-0.253j -0.215-0.216j -0.058-0.47j -0.138+0.258j 0.462-0.392j]]\n"
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]
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}
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],
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[[ 0.240-0.126j -0.439-0.47j -0.689+0.195j]\n",
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" [ 0.900+0.065j -0.208+0.072j 0.357-0.101j]\n",
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" [ 0.335+0.j 0.683+0.268j -0.371+0.461j]]\n",
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"\n",
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"[ 0.457+0.889j -0.916-0.4j 0.970-0.242j]\n"
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"[[ 0.912+0.068j -0.077+0.112j -0.297-0.239j]\n",
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" [ 0.181-0.096j -0.806-0.128j 0.420+0.339j]\n",
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" [ 0.349+0.j 0.561-0.019j 0.698+0.276j]]\n",
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"()\n",
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"[-0.209+0.978j -0.714-0.7j -0.645+0.764j]\n"
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]
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}
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],
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"('2, 3, 0.671, -2.644',)\n",
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"('1, 2, 1.421, 0.281', '3, 4, 1.401, -1.617')\n",
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"('0, 1, 0.683, -2.284', '2, 3, 0.704, 2.724', '4, 5, 1.204, 2.049')\n",
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"('1, 2, 0.800, -2.721', '3, 4, 1.412, -2.494')\n",
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"('2, 3, 1.112, -3.003',)\n"
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"('2, 3, 0.172, -0.438',)\n",
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"('1, 2, 1.212, 2.149', '3, 4, 0.313, 1.750')\n",
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"('0, 1, 0.986, 2.937', '2, 3, 1.062, 1.518', '4, 5, 1.106, 2.647')\n",
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"('1, 2, 0.945, -0.406', '3, 4, 1.190, -0.769')\n",
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"('2, 3, 1.339, -1.335',)\n"
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]
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}
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],
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[[ 0.355+0.69j -0.035+0.087j 0.301-0.385j 0.356-0.154j 0.000+0.j 0.000+0.j ]\n",
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" [-0.403-0.176j -0.340-0.323j -0.081-0.496j 0.192-0.297j 0.165-0.427j 0.000-0.j ]\n",
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" [ 0.194-0.048j -0.169-0.072j 0.242+0.25j -0.064-0.069j -0.088-0.325j 0.704-0.432j]]\n"
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"[[-0.115+0.54j -0.002+0.292j 0.642+0.425j -0.132-0.02j -0.000+0.j 0.000-0.j ]\n",
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" [-0.349-0.342j 0.440+0.195j 0.198-0.152j -0.102-0.64j -0.192-0.104j 0.000+0.j ]\n",
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" [-0.100+0.118j -0.176-0.211j 0.111-0.117j 0.298-0.182j -0.142+0.282j 0.765-0.26j ]]\n"
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]
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}
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],
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"output_type": "stream",
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"text": [
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"Number of rotations to perform in parallel: 1\n",
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"[[ 0.355+0.69j -0.035+0.087j 0.384-0.491j 0.000-0.j 0.000+0.j 0.000+0.j ]\n",
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" [-0.403-0.176j -0.340-0.323j -0.047-0.607j -0.072-0.032j 0.165-0.427j 0.000-0.j ]\n",
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" [ 0.194-0.048j -0.169-0.072j 0.134+0.177j 0.220+0.179j -0.088-0.325j 0.704-0.432j]]\n",
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"\n",
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"[[-0.115+0.54j -0.002+0.292j 0.651+0.431j 0.000+0.j -0.000+0.j 0.000-0.j ]\n",
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" [-0.349-0.342j 0.440+0.195j 0.164-0.043j 0.210-0.64j -0.192-0.104j 0.000+0.j ]\n",
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" [-0.100+0.118j -0.176-0.211j 0.050-0.108j 0.361-0.058j -0.142+0.282j 0.765-0.26j ]]\n",
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"()\n",
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"Number of rotations to perform in parallel: 2\n",
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"[[ 0.355+0.69j -0.236+0.585j 0.000-0.j 0.000-0.j 0.000-0.j 0.000+0.j ]\n",
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" [-0.403-0.176j 0.160+0.516j -0.368-0.405j -0.425-0.187j 0.000+0.j 0.000-0.j ]\n",
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" [ 0.194-0.048j -0.201-0.142j -0.140-0.051j -0.287+0.102j 0.272+0.164j 0.704-0.432j]]\n",
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"\n",
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"[[-0.115+0.54j -0.005+0.834j -0.000+0.j 0.000-0.j 0.000+0.j 0.000-0.j ]\n",
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" [-0.349-0.342j 0.272+0.175j 0.368+0.143j 0.221-0.672j 0.000+0.j 0.000+0.j ]\n",
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" [-0.100+0.118j 0.049-0.09j -0.206-0.192j 0.250-0.083j 0.400+0.068j 0.765-0.26j ]]\n",
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"()\n",
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"Number of rotations to perform in parallel: 3\n",
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"[[ 0.457+0.889j -0.000+0.j 0.000-0.j 0.000-0.j 0.000+0.j 0.000-0.j ]\n",
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" [-0.000-0.j -0.638-0.279j -0.483-0.531j -0.000-0.j 0.000-0.j 0.000+0.j ]\n",
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" [ 0.000+0.j 0.308-0.077j -0.303-0.054j 0.141-0.015j 0.759+0.457j 0.000+0.j ]]\n",
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"\n",
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"[[-0.209+0.978j -0.000+0.j -0.000+0.j -0.000-0.j 0.000+0.j 0.000-0.j ]\n",
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" [ 0.000-0.j -0.418-0.41j 0.756+0.293j 0.000-0.j 0.000+0.j 0.000+0.j ]\n",
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" [ 0.000-0.j -0.120+0.142j -0.039+0.129j -0.214-0.291j 0.891+0.151j -0.000+0.j ]]\n",
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"()\n",
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"Number of rotations to perform in parallel: 2\n",
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"[[ 0.457+0.889j -0.000-0.j -0.000+0.j 0.000+0.j -0.000-0.j 0.000-0.j ]\n",
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" [-0.000-0.j -0.916-0.4j 0.000+0.j 0.000-0.j -0.000-0.j 0.000+0.j ]\n",
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" [ 0.000+0.j -0.000-0.j 0.429-0.107j 0.892-0.095j 0.000-0.j 0.000+0.j ]]\n",
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"\n",
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"[[-0.209+0.978j 0.000-0.j -0.000+0.j -0.000-0.j -0.000-0.j 0.000-0.j ]\n",
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" [ 0.000-0.j -0.714-0.7j -0.000+0.j 0.000-0.j 0.000-0.j 0.000+0.j ]\n",
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" [ 0.000-0.j -0.000-0.j -0.148+0.175j -0.576-0.784j -0.000-0.j -0.000+0.j ]]\n",
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"()\n",
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"Number of rotations to perform in parallel: 1\n",
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"[[ 0.457+0.889j -0.000-0.j -0.000+0.j -0.000+0.j -0.000-0.j 0.000-0.j ]\n",
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" [-0.000-0.j -0.916-0.4j 0.000-0.j 0.000+0.j -0.000-0.j 0.000+0.j ]\n",
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" [ 0.000+0.j -0.000-0.j 0.970-0.242j -0.000-0.j 0.000-0.j 0.000+0.j ]]\n",
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"\n"
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"[[-0.209+0.978j 0.000-0.j -0.000+0.j -0.000+0.j -0.000-0.j 0.000-0.j ]\n",
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" [ 0.000-0.j -0.714-0.7j -0.000+0.j -0.000+0.j 0.000-0.j 0.000+0.j ]\n",
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" [ 0.000-0.j -0.000-0.j -0.645+0.764j 0.000+0.j -0.000-0.j -0.000+0.j ]]\n",
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"()\n"
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]
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 2",
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"language": "python",
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"name": "python3"
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"name": "python2"
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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"version": 2
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.2"
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"pygments_lexer": "ipython2",
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"version": "2.7.13"
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"nbformat": 4,

‎examples/openfermion_demo.ipynb‎

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‎examples/performance_benchmarks.py‎

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import numpy
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import time
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from openfermion.ops import FermionOperator, InteractionOperator, normal_ordered
17+
from openfermion.ops import (FermionOperator,
18+
InteractionOperator,
19+
normal_ordered)
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from openfermion.transforms import get_fermion_operator, jordan_wigner
1921
from openfermion.utils import jordan_wigner_sparse
2022

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188190
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190192
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191-
'takes {} seconds on {} qubits.'.format(runtime, n_qubits))
193+
'takes {} seconds on {} qubits.\n'.format(runtime, n_qubits))
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199201
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202+
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# Run FermionOperator.jordan_wigner_sparse() benchmark.

‎src/openfermion/_version.py‎

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# limitations under the License.
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"""Define version number here and read it from setup.py automatically"""
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__version__ = "0.1a1"
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__version__ = "0.1a2"

‎src/openfermion/hamiltonians/__init__.py‎

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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
4+
#
5+
# http://www.apache.org/licenses/LICENSE-2.0
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#
7+
# Unless required by applicable law or agreed to in writing, software
8+
# distributed under the License is distributed on an "AS IS" BASIS,
9+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10+
# See the License for the specific language governing permissions and
11+
# limitations under the License.
12+
13+
from ._chemical_series import (make_atomic_ring,
14+
make_atomic_lattice,
15+
make_atom)
16+
17+
from ._hubbard import fermi_hubbard
18+
19+
from ._jellium import (dual_basis_kinetic,
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dual_basis_potential,
21+
dual_basis_jellium_model,
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jellium_model,
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jordan_wigner_dual_basis_jellium,
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plane_wave_kinetic,
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plane_wave_potential)
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from ._mean_field_dwave import mean_field_dwave
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from ._molecular_data import MolecularData, periodic_table
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from ._plane_wave_hamiltonian import (dual_basis_external_potential,
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plane_wave_external_potential,
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plane_wave_hamiltonian,
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jordan_wigner_dual_basis_hamiltonian,
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wigner_seitz_length_scale)

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