# Pennylane takes too long to build a Hamiltonian **URL:** \ **Category:** PennyLane Help\ **Created:** [October 20, 2022, 8:47pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234 "2022-10-20T20:47:55Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![Einar\_Gabbassov](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/einar_gabbassov/32/576_2.png) [@Einar\_Gabbassov](https://discuss.pennylane.ai/u/Einar_Gabbassov)\ **Post date:** [October 20, 2022, 8:47pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/1 "2022-10-20T20:47:55Z")
Dear Pennylane team, I’ve buid a number of molecular Hamiltonians and quantum circuits by using the calls `qchem.molecular_hamiltonian()` and `ApproxTimeEvolution()`. Most molecules I’ve tried are toy examples and featured in the Pennylane tutorials or documentation pages. I’ve tried: LiH, H2O and H2. For these small molecules Pennylane computes Hamiltonians and respective quantum circuits in few minutes. However, recently I’ve tried to get a Hamiltonian and a quantum circuit for the C2HF3 molecule. The geometry is as follows: ```auto symbols = ["C", "C", "F", "F", "F", "H"] coordinates = np.array( [ 0.0, 0.430631, 0.000000, -0.704353, -0.686847, 0.0, 1.314791, 0.500587, 0.0, -0.554822, 1.630861, 0.0, -0.092517, -1.882156, 0.0, -1.780948, -0.706341, 0.0 ] ) hamiltonian, num_qubits = qchem.molecular_hamiltonian(symbols, coordinates) print(f"Number of qubits: {num_qubits}") print("Qubit Hamiltonian") print(hamiltonian) ``` This is a larger molecule and Pennylane is not able to compute a Hamiltonian let alone the circuit. That is, calling `qchem.molecular_hamiltonian()` runs for hours and never terminates. Any ideas on how to get a Hamiltonian and a circuit in reasonable time (say few minutes)? What do I miss here? P.S. I tried the same molecule in a different quantum chem python package and it was able to produce a Hamiltonian and a respective circuit in under 2 minutes. ---
**Author:** ![CatalinaAlbornoz](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/catalinaalbornoz/32/1196_2.png) [@CatalinaAlbornoz](https://discuss.pennylane.ai/u/CatalinaAlbornoz)\ **Post date:** [October 21, 2022, 10:08pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/2 "2022-10-21T22:08:25Z")
Hi @Einar_Gabbassov, Thank you for sharing this information with us. The molecule you’re looking at is quite large so my guess is that any other packages you’re using are doing approximations or using qubit-reduction techniques under the hood. Something you could try is doing qubit tapering. This can reduce your computational needs and speed up the simulation. You can learn more about this in [this demo](https://pennylane.ai/qml/demos/tutorial_qubit_tapering.html). Please let me know if you have any questions about this and let me know if this gives you a speedup! ---
**Author:** ![CatalinaAlbornoz](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/catalinaalbornoz/32/1196_2.png) [@CatalinaAlbornoz](https://discuss.pennylane.ai/u/CatalinaAlbornoz)\ **Post date:** [October 24, 2022, 3:01pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/3 "2022-10-24T15:01:14Z")
Hi @Einar_Gabbassov, My colleague Soran suggested that you will get much better speed if you use `method="pyscf"` when you build the molecular Hamiltonian. So you would do something like: `H, qubits = qchem.molecular_hamiltonian(symbols, coordinates, method="pyscf")` You can learn more about this in [this demo](https://pennylane.ai/qml/demos/tutorial_quantum_chemistry.html#openfermion-pyscf-backend). I hope this is helpful! ---
**Author:** ![Einar\_Gabbassov](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/einar_gabbassov/32/576_2.png) [@Einar\_Gabbassov](https://discuss.pennylane.ai/u/Einar_Gabbassov)\ **Post date:** [October 25, 2022, 11:04pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/4 "2022-10-25T23:04:53Z")
Hi @CatalinaAlbornoz Thanks for the suggestion. I have tried `method=pyscf`. Unfortunattely, it crashes my jupyter notebook and on top of that it produces an error. On a positive side… it takes about 5 minutes to crash my jupyter notebook. So if the bug is fixed, it might take about 5 minutes to compute the Hamiltonian?? 🤷‍♂️ Below is a partial traceback. Note that even though all coefficients of a Hamiltonian are real, the datatype seems to be a complex number. ```auto File ~/.pyenv/versions/circuit_comp_env/lib/python3.8/site-packages/pennylane/qchem/openfermion_obs.py:956, in molecular_hamiltonian(symbols, coordinates, name, charge, mult, basis, method, active_electrons, active_orbitals, mapping, outpath, wires, alpha, coeff, args, grouping_type, grouping_method) 950 core, active = qml.qchem.active_space( 951 molecule.n_electrons, molecule.n_orbitals, mult, active_electrons, active_orbitals 952 ) 954 h_of, qubits = (decompose(hf_file, mapping, core, active), 2 * len(active)) --> 956 h_pl = qml.qchem.convert.import_operator(h_of, wires=wires) 958 return ( 959 qml.Hamiltonian(h_pl.coeffs, h_pl.ops, grouping_type=grouping_type, method=grouping_method), 960 qubits, 961 ) File ~/.pyenv/versions/circuit_comp_env/lib/python3.8/site-packages/pennylane/qchem/convert.py:325, in import_operator(qubit_observable, format, wires, tol) 320 raise TypeError(f"Converter does not exist for {format} format.") 322 if any( 323 np.iscomplex(np.real_if_close(coef, tol=tol)) for coef in qubit_observable.terms.values() 324 ): --> 325 raise TypeError( 326 f"The coefficients entering the QubitOperator must be real;" 327 f" got complex coefficients in the operator {qubit_observable}" 328 ) 330 return qml.Hamiltonian(*_openfermion_to_pennylane(qubit_observable, wires=wires)) TypeError: The coefficients entering the QubitOperator must be real; got complex coefficients in the operator (-169.0923877964394+0j) [] + (-3.41902239433203e-05+0j) [X0 X1 Y2 Y3] + (-2.996469373464669e-06+0j) [X0 X1 Y2 Z3 Z4 Y5] + ... ... ``` ---
**Author:** ![CatalinaAlbornoz](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/catalinaalbornoz/32/1196_2.png) [@CatalinaAlbornoz](https://discuss.pennylane.ai/u/CatalinaAlbornoz)\ **Post date:** [October 26, 2022, 10:27pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/5 "2022-10-26T22:27:05Z")
Hi @Einar_Gabbassov, thank you for posting this here. Is this the full error traceback? Also, can you please post the output of qml.about()? ---
**Author:** ![CatalinaAlbornoz](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/catalinaalbornoz/32/1196_2.png) [@CatalinaAlbornoz](https://discuss.pennylane.ai/u/CatalinaAlbornoz)\ **Post date:** [October 26, 2022, 10:45pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/6 "2022-10-26T22:45:33Z")
Hi @Einar_Gabbassov, I managed to reproduce your problem. I will look into it and come back with an answer. ---
**Author:** ![sjahangiri](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/sjahangiri/32/1443_2.png) [@sjahangiri](https://discuss.pennylane.ai/u/sjahangiri)\ **Post date:** [October 28, 2022, 6:45pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/7 "2022-10-28T18:45:44Z")
Hi @Einar_Gabbassov and thanks for using PennyLane to simulate this interesting molecule. The molecule is relatively large and it is more efficient to use the non-differentiable workflow of PennyLane, which uses OpenFermion-PySCF, to construct the molecular Hamiltonian. Please see [here](https://pennylane.ai/qml/demos/tutorial_quantum_chemistry.html#openfermion-pyscf-backend) and [here](https://pennylane.ai/qml/demos/tutorial_differentiable_HF.html) for more details. The error you get is because of small imaginary components in the Hamiltonian coefficients. The default threshold for raising this error is defined [here](https://github.com/PennyLaneAI/pennylane/blob/623d76b8c3d1fc52607b79a589468bed9bd49079/pennylane/qchem/convert.py#L287). We are working on making this default threshold slightly larger. In the meantime, you can directly construct your Hamiltonian using the following code. Please note that the atomic coordinates should be in atomic units and a [conversion factor](https://physics.nist.gov/cgi-bin/cuu/Value?bohrrada0) must be applied to the original values. ``` import pennylane as qml from pennylane import numpy as np import openfermion from pennylane.qchem.openfermion_obs import meanfield, decompose symbols = ["C", "C", "F", "F", "F", "H"] coordinates = np.array( [ 0.0, 0.430631, 0.000000, -0.704353, -0.686847, 0.0, 1.314791, 0.500587, 0.0, -0.554822, 1.630861, 0.0, -0.092517, -1.882156, 0.0, -1.780948, -0.706341, 0.0 ] ) / 0.529177210903 # convert to Bohr hf_file = meanfield(symbols, coordinates) molecule = openfermion.MolecularData(filename=hf_file) h_of = decompose(hf_file) h_pl = qml.qchem.convert.import_operator(h_of, tol=1e09) # use a larger threshold for the imaginary part print(h_pl) ``` Please feel free to let us know if you have any further questions. ---
**Author:** ![morgoth](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/morgoth/32/1777_2.png) [@morgoth](https://discuss.pennylane.ai/u/morgoth)\ **Post date:** [November 30, 2023, 8:10pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/8 "2023-11-30T20:10:35Z")
Isn’t possible to parallelize the Hamiltonian building? ---
**Author:** ![isaacdevlugt](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/isaacdevlugt/32/1159_2.png) [@isaacdevlugt](https://discuss.pennylane.ai/u/isaacdevlugt)\ **Post date:** [December 4, 2023, 2:51pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/9 "2023-12-04T14:51:10Z")
Hey @morgoth! PennyLane doesn’t have anything to support building a Hamiltonian in parallel. You might have luck with using some external libraries like Dask, but I’m not sure if they will work as intended. You can look at some of our support for parallelization here: - [PennyLane v0.31 released | PennyLane Blog](https://pennylane.ai/blog/2023/06/pennylane-release-0.31/#gpu-distributed-statevector-support-) - [Lightning plugins — Lightning 0.33.1 documentation](https://docs.pennylane.ai/projects/lightning/en/stable/index.html) ---
**Author:** ![morgoth](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/morgoth/32/1777_2.png) [@morgoth](https://discuss.pennylane.ai/u/morgoth)\ **Post date:** [December 8, 2023, 10:46pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/10 "2023-12-08T22:46:57Z")
Hi @isaacdevlugt! Thank you for replying. If it’s possible, I’d like to suggest that the development team think about implementing something like this. Pyscf reduces processing time, but it’s a non-differentiable backend, so it may not be suitable in some cases. ---
**Author:** ![isaacdevlugt](https://yyz2.discourse-cdn.com/flex012/user_avatar/discuss.pennylane.ai/isaacdevlugt/32/1159_2.png) [@isaacdevlugt](https://discuss.pennylane.ai/u/isaacdevlugt)\ **Post date:** [December 11, 2023, 2:30pm UTC](https://discuss.pennylane.ai/t/pennylane-takes-too-long-to-build-a-hamiltonian/2234/11 "2023-12-11T14:30:23Z")
Definitely! I suggest that you make a feature request on our repository so that we can try to fit this in if it’s possible 🙂. You can use this link 🔽 > **[Build software better, together](https://github.com/PennyLaneAI/pennylane/issues/new?assignees=&labels=enhancement%2B%3Asparkles%3A&projects=&template=feature_request.yml)** > > GitHub is where people build software. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects.