Comments (8)
lkwagner
commented on September 4, 2024
Hi David,
Thanks for the issue! The documentation has been updated there. You might find the HOWTOs more useful than the developer documentation:
https://pyqmc.readthedocs.io/en/latest/snippets.html
We currently don't support CISD wave functions natively. See Issue #241 It is possible to construct a determinant list by hand, if you like. It wouldn't be too hard to do that.
However, these days we don't typically use CISD because it's almost always worse than HCI or CASSCF/CASCI. You will probably get similar results to the article if you do something like the following, which will get you the ground-state Jastrow:
def run_casci(scf_checkfile, ci_checkfile):
mol, mf = pyq.recover_pyscf(scf_checkfile, cancel_outputs=False)
mc = mcscf.CASCI(mf, 6, 6)
mc.nroots=12
mc.kernel()
with h5py.File(ci_checkfile, "a") as f:
f.create_group("mc")
f["mc/ncas"] = mc.ncas
f["mc/nelecas"] = list(mc.nelecas)
f["mc/ci"] = mc.ci
f["mc/mo_coeff"] = mc.mo_coeff
return mc
if __name__ == "__main__":
run_mf("mf.chk")
run_casscf("mf.chk", "cas.chk")
pyq.OPTIMIZE("mf.chk", "opt.chk", ci_checkfile="cas.chk", nconfig=1000)
After that, you will want to attach the ground state Jastrow to the CAS roots to get approximate excited states. I have some examples of that somewhere, but let me know if this works for you.
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davidsousarj
commented on September 4, 2024
Hi @lkwagner .
I tried to run these lines of code but it does not work. Here is the error message:
Traceback (most recent call last):
File "/home/david/MEGA/ACADÊMICO/A_POST_DOC_EUA/QMC/6_Benzene_LucasWagner.py", line 122, in <module>
pyq.OPTIMIZE("mf.chk", "opt.chk", ci_checkfile="cas.chk", nconfig=1000)
File "/home/david/.local/lib/python3.10/site-packages/pyqmc/recipes.py", line 45, in OPTIMIZE
wf, configs, acc = initialize_qmc_objects(
File "/home/david/.local/lib/python3.10/site-packages/pyqmc/recipes.py", line 186, in initialize_qmc_objects
mol, mf, mc = pyscftools.recover_pyscf(dft_checkfile, ci_checkfile=ci_checkfile)
File "/home/david/.local/lib/python3.10/site-packages/pyqmc/pyscftools.py", line 69, in recover_pyscf
if len(casdict["mo_coeff"].shape) == 3:
TypeError: 'NoneType' object is not subscriptable
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willwheelera
commented on September 4, 2024
Hi David, I apologize for the confusion. The example code I added to the documentation was outdated. Could you try this instead? The label "mc" is changed to "ci"
def run_casci(scf_checkfile, ci_checkfile):
mol, mf = pyq.recover_pyscf(scf_checkfile, cancel_outputs=False)
mc = mcscf.CASCI(mf, 2, 2)
mc.kernel()
with h5py.File(ci_checkfile, "a") as f:
f.create_group("ci")
f["ci/ncas"] = mc.ncas
f["ci/nelecas"] = list(mc.nelecas)
f["ci/ci"] = mc.ci
f["ci/mo_coeff"] = mc.mo_coeff
return mc
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davidsousarj
commented on September 4, 2024
Hi @willwheelera . I tried this one. Now it raises other error message:
Traceback (most recent call last):
File "/home/david/MEGA/ACADÊMICO/A_POST_DOC_EUA/QMC/6_Benzene_LucasWagner.py", line 133, in <module>
pyq.OPTIMIZE("mf.chk", "opt.chk", ci_checkfile="cas.chk", nconfig=1000)
File "/home/david/.local/lib/python3.10/site-packages/pyqmc/recipes.py", line 45, in OPTIMIZE
wf, configs, acc = initialize_qmc_objects(
File "/home/david/.local/lib/python3.10/site-packages/pyqmc/recipes.py", line 189, in initialize_qmc_objects
elif mc.orbitals is None:
AttributeError: 'CASCI' object has no attribute 'orbitals'
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willwheelera
commented on September 4, 2024
Hi David, thanks for trying that and following up. I recognize where your error is coming from, and I think our current version of the code no longer does that. Can you try it again using the current version? If you installed with pip, you can do pip install git+git://github.com/WagnerGroup/pyqmc --upgrade
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davidsousarj
commented on September 4, 2024
Thank you @willwheelera . I tried to install using pip but it did not work for some reason. Then I downloaded the zip file from github and installed it manually.
I am sorry, but it is still not working. There is another error now:
Traceback (most recent call last):
File "/home/dms7983/MEGAsync/ACADÊMICO/A_POST_DOC_EUA/QMC/6_Benzene_LucasWagner.py", line 127, in <module>
pyq.OPTIMIZE("mf.chk", "opt.chk", ci_checkfile="cas.chk", nconfig=1000)
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/recipes.py", line 45, in OPTIMIZE
wf, configs, acc = initialize_qmc_objects(
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/recipes.py", line 199, in initialize_qmc_objects
wf, to_opt = wftools.generate_wf(
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/wftools.py", line 157, in generate_wf
wf1, to_opt1 = generate_slater(mol, mf, mc=mc, **slater_kws)
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/wftools.py", line 28, in generate_slater
wf = slater.Slater(mol, mf, **kwargs)
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/slater.py", line 166, in __init__
) = pyqmc.orbitals.choose_evaluator_from_pyscf(
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/orbitals.py", line 59, in choose_evaluator_from_pyscf
return MoleculeOrbitalEvaluator.from_pyscf(
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/orbitals.py", line 87, in from_pyscf
detcoeff, occup, det_map = pyqmc.determinant_tools.interpret_ci(mc, tol)
File "/home/dms7983/.local/lib/python3.10/site-packages/pyqmc/determinant_tools.py", line 69, in interpret_ci
deters = fci.addons.large_ci(mc.ci, mc.ncas, mc.nelecas, tol=-1)
File "/home/dms7983/.local/lib/python3.10/site-packages/pyscf/fci/addons.py", line 36, in large_ci
assert (ci.shape == (na, nb))
AssertionError
I will send you my script just to make sure I am not doing anything wrong.
6_Benzene_LucasWagner.py.txt
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willwheelera
commented on September 4, 2024
Hi David, thanks for following up and thanks for your patience with all the errors.
We just added a fix that I think should solve this error. Could you try it again with the update?
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davidsousarj
commented on September 4, 2024
@willwheelera sorry for the delay. I run the script but it took over 24 hours to finish. It run without errors.
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Related Issues (20)
- J3.py has no testvalue_many attribute HOT 1
- Broken documentation
- Documentation error HOT 1
- New timestep algorithm? HOT 1
- compute variance
- Implement ensemble excited state optimization from Entwistle et al HOT 1
- distance function dist_i is confusing HOT 1
- Implement orbital evaluation HOT 3
- Conditional wave function package
- Unexpected kpts property generated by RKS() leading to UnboundLocalError in determinant_tools.py
- Abstract Base Classes for better documentation
- Attribute error in PeriodicConfigs object HOT 2
- Significant increase in energy with wavefunction optimization HOT 5
- Support batch optimization in linemin HOT 2
- sample_many should take a dictionary
- a problem with 3-body Jastrow factor HOT 3
- GeminalJastrow missing testvalue_many HOT 1
- ThreeBodyJastrow missing testvalue_many
- Question Regarding T-Moves Implementation in PyQMC HOT 4
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