Need more details on the jobs

[rwest]

@ehermes just posted via the sandia gitlab thing:

Can you specify more details about the jobs? What level of theory, what basis set, etc...

[nateharms]

M06-2X/6-311+g(2df,2p) or better please

[nateharms]

Or the 6-311+g** basis set if the 6-311+g(2df,2p) basis set is unavailable

[ehermes]

I'll try out a few of these calculations to benchmark, but compared to the 6480 saddle point searches I'm already running, your tests are using a more expensive level of theory (I'm using B3LYP/6-31G) and have some larger molecules (my biggest molecules have 8 heavy atoms). There's a chance that your tests will scale better on KNL though, since they're bigger.

Are all of these tests closed-shell? If not, how can I tell which are open shell and which are closed-shell?

[rwest]

I believe they're all H-abstraction, so will all have a radical involved.

[ehermes]

Well, I found at least one geometry where NWChem said a multiplicity of 2 was invalid. I suppose I can just count the number of hydrogens and determine the multiplicity that way.

[ehermes]

Since all of the reactions are H-abstractions, does that mean systems with an even number of electrons should have a multiplicity of 3?

[rwest]

@nateharms are some of them abstracting H from a radical, and thus have an even number of electrons overall?

(And did you include abstraction by triplet O₂?)

[nateharms]

• all reactions are H-Abstraction
• some reactions are H-abstractions involving two radicals (e.g. OOH abstracting from [CH2]CC or something)
• some reactions involve abstraction by triplet O2

[ehermes]

Can you give me some advice on how to determine which multiplicity to use for which geometries?

[nateharms]

Would it be easier if I provided a text file containing a dictionary of files and their corresponding multiplicity?

[ehermes]

If you can provide the multiplicities for each geometry, that would certainly be helpful.

[nateharms]

Okay, a text file has been added with corresponding file names and their multiplicities

[ehermes]

These calculations are going to take a lot of time. Unfortunately, NWChem's DFT routines (LCAO, not plane waves) are not at all optimized for many-core systems like Theta. Since the calculations in my test set are all fairly inexpensive, this wasn't a big problem, but testing M06-2X/6-311++G** I am seeing calculations take 10 minutes per single point on 2 nodes (128 cores). It will be difficult to do a meaningful amount of work in the span of a single job, given the very low time limits for jobs on Theta.

My priority currently is getting my own test set completed. Once they are done, I can start working on these systems. I think it will be a lot easier to first optimize the saddle points using a less expensive level of theory, then re-optimize at M06-2X/6-311++G** -- possibly on a different cluster.

[nateharms]

Gotcha, how about run M06-2X/6-31G? Will that be less expensive? Either that or run it whatever you think seems suitable, we can re-optimize them later. Thanks for the help!

[ehermes]

I'll test a couple of different things to see if I can find something reasonably fast that is close to your desired settings. M06-2X being a meta-GGA also adds a nontrivial cost, particularly in terms of SCF convergence (Truhlar's functionals have notorious convergence difficulties).

[ehermes]

I've started running these calculations now. I'm going to start by optimizing the saddle points with B3LYP/6-31G, then refining with M06-2X/6-311+G**.

I noticed there is a med directory as well, but these structure multiplicities are not in mults.txt. Do you want me to run these structures as well? If so, can you provide their multiplicities?

[nateharms]

@ehermes an updated mults.py file exists containing the multiplicities for all the files

[ehermes]

I'm having trouble parsing this file automatically. It seems like there's a strange character on line 2859.

[nateharms]

Hmmm... I'm not sure why it isn't working... I'm able to read in the file easily. But I'll try writing a new file and seeing if that helps

[nateharms]

@ehermes a file called mults.csv file was added. I didn't have any trouble reading it in with pandas. Hope this helps!

[rwest]

Some seem to be missing:

import pandas
import os
df = pandas.read_csv('mults.csv')
for dirpath, dirnames, filenames in os.walk('.'):
    if './' not in dirpath or '.git' in dirpath: continue
    _,d = dirpath.split('/')
    for f in filenames:
        if '.xyz' not in f:
            continue
        p = os.path.join(d,f)
        found = (sum(df.file_name==p))
        if found !=1:
            print(p, found)

high/C=CC=C+[O]O_C=[C]C=C+OO.xyz 0
high/[O]O+[CH2]CCC_CCCC+[O][O].xyz 0
low/C=CCC+[CH]=C_C=[C]CC+C=C.xyz 0
low/[O]OC=O+CC(C)(C)O_O=COO+CC(C)(C)[O].xyz 0
low/CO+CCCCO[O]_[CH2]O+CCCCOO.xyz 0
low/CCCO[O]+C=CC_CCCOO+[CH]=CC.xyz 0
low/CC(C)O[O]+CC=O_CC(C)OO+C[C]=O.xyz 0
low/C[C]=O+CCC(C)O_CC=O+C[CH]C(C)O.xyz 0
low/C#CC+[O][O]_C#C[CH2]+[O]O.xyz 0
low/[CH2]O+CCCC_CO+C[CH]CC.xyz 0
low/[CH3]+C=C=O_C+[CH]=C=O.xyz 0
med/[CH3]+CC(C)CC(=O)CC(C)C_[CH2]C(C)CC(=O)CC(C)C+C.xyz 0
med/[OH]+CCCC(C)CO_CCCC(C)[CH]O+O.xyz 0
med/[H]+CCCC=CC(C)C_C[CH]CC=CC(C)C+[H][H].xyz 0
med/[H]+CCC(C)CC(C)C_[H][H]+CCC(C)[CH]C(C)C.xyz 0
med/[H]+CCCCCC1CCC(C)O1_CCCCCC1C[CH]C(C)O1+[H][H].xyz 0

[nateharms]

@rwest thanks for the catch, should be good now 👍