Currently prepare_hamiltonian.py does not create certain files. For example, when H[i,j] = 0.0, it does save the corresponding H.{i+1}.{j+1}.dat file. Is this an intended design? I can see some scenarios where it might be problematic:
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It is fine when i !=j, but sometimes we want some diabatic PESs to be zero, i.e., H[i,i]=0, in which case the lack of an H.{i+1}.{i+1}.dat file will throw up an error for Qdyn.
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Perhaps more dangerous is when one modifies the Hamiltonian such that some other H[j,j] is set to 0. In this case, qdyn will simply use the existing H.{j+1}.{j+1}.dat file, which will not contain zeros, as intended.
Can we always force that all H.{i+1}.{j+1}.dat files to always be (re)written every time prepare_hamiltonian.py is run?
Currently
prepare_hamiltonian.pydoes not create certain files. For example, when H[i,j] = 0.0, it does save the corresponding H.{i+1}.{j+1}.dat file. Is this an intended design? I can see some scenarios where it might be problematic:It is fine when i !=j, but sometimes we want some diabatic PESs to be zero, i.e., H[i,i]=0, in which case the lack of an H.{i+1}.{i+1}.dat file will throw up an error for Qdyn.
Perhaps more dangerous is when one modifies the Hamiltonian such that some other H[j,j] is set to 0. In this case, qdyn will simply use the existing H.{j+1}.{j+1}.dat file, which will not contain zeros, as intended.
Can we always force that all H.{i+1}.{j+1}.dat files to always be (re)written every time
prepare_hamiltonian.pyis run?