Q2DTor Integration by mjohnson541 · Pull Request #1585 · ReactionMechanismGenerator/RMG-Py

mjohnson541 · 2019-04-24T22:33:54Z

This PR enables 2D dimensional coupled rotor calculations using the 2D-NS approximation within Arkane using the external software Q2DTor written by David Ferro Costas and Antonio Fernandez Ramos. It adds a wrapper class in Arkane for computing the statistical mechanical properties of 2D coupled rotors using Q2DTor and adds rotor processing for 2D coupled rotors.

Installing my fork of Q2DTor:

git clone https://github.com/mjohnson541/Q2DTor.git
git checkout arkane

add to your .bashrc or .bash_profile (as appropriate):
export Q2DTor=/.../Q2DTor/src/Q2DTor.py (replacing ... with appropriate absolute path)

I've added an example for calculating the thermo of CH2CHOOH. However the full example takes ~5-8 hours of time to run. The wrapper (HinderedRotor2D) automatically checks for the presence of the .evals output file from Q2DTor that contains the eigenvalues of the Hamiltonian. If it finds this file it automatically skips the calculations and uses the eigenvalues to compute statistical mechanical properties. To shorten the example I've added all of the Q2DTor output files to the example allowing it to find the .evals file and finish rapidly.

I haven't added the documentation yet, primarily because I haven't decided on answers to the following questions yet:

How much detail should we have in the documentation specifically on Q2DTor's internals
Where should Q2DTor details be located
Where should the installation instructions go?

…object

calcPath is the a directory containing rotor calculations named: scangeom_{name}_{phi1}_{phi2}.out and input files scangeom_{name}_{phi1}_{phi2}.gjf automatically constructs a directory based on self.name to run Q2DTor in

…iles

…priate files

…s file

…n the energy levels of the 2D-NS partition function

…rotors so that statmech properties can be calculated

codecov · 2019-04-29T16:22:31Z

Codecov Report

Merging #1585 into master will increase coverage by 0.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #1585      +/-   ##
==========================================
+ Coverage   41.58%   41.59%   +0.01%     
==========================================
  Files         176      176              
  Lines       29147    29147              
  Branches     5995     5995              
==========================================
+ Hits        12120    12125       +5     
+ Misses      16187    16183       -4     
+ Partials      840      839       -1

Impacted Files	Coverage Δ
rmgpy/data/kinetics/family.py	`52.97% <0%> (+0.23%)`	⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bf2d163...76a56ed. Read the comment docs.

alongd

I haven't reviewed all commits yet, but wanted these comments to be uploaded for now. Perhaps take them into account when you modify the PR as you suggested offline?

alongd · 2019-04-30T16:34:51Z

rmgpy/statmech/conformer.pyx

 cdef class Conformer(RMGObject):
    """
-    A representation of an individual molecular conformation. The attributes 
+    A representation of an individual molecular conformation. The attributes


Would you like to make a separate commit for all the white space fixes?

white space changes removed

alongd · 2019-04-30T16:38:08Z

arkane/statmech.py

           pass

+
+   def readScan(self):


This is implemented for a 2D rotor (specifically from Q2DTor). Should the function name reflect that it's a 2D rotor?

Sorry, I'll clean up the order...not sure how it got this out of order

alongd · 2019-04-30T16:39:46Z

arkane/statmech.py

+       for f in os.listdir(self.calcPath):
+           if len(f.split('_')) != 4:
+               continue
+           s,name,phi1,phi2 = f.split('_')


Could you add a comment with an example of such a file name for easier future readability and debugging?
We're checking above for four _, but I see three in scangeom_{name}_{phi1}_{phi2}.out

Splitting on three '_' will give you a four-tuple => (scangeom, name, phi1, phi2.out)

alongd · 2019-04-30T18:28:45Z

arkane/statmech.py

+           Es.append(lg.software_log.loadEnergy())
+           xyz,atnum,_ = lg.software_log.loadGeometry()
+           xyzs.append(xyz)
+           atnums.append(atnum)


atom numbers shouldn't change. Do you think we can just parse it once?

I don't think you can really avoid parsing it, but I can just store it once.

alongd · 2019-04-30T18:30:16Z

arkane/statmech.py

                     ' based on the {3}.'.format(symmetry, label, pivots, reason))
    return symmetry
+
+class HinderedRotor2D(Mode):


Should this go to rmgpy.statmech.mode?

It would make most sense to place it in rmgpy.statmech.torsion.pyx, but it creates a cyclic import I could resolve related to loading qm files, I think statmech.py is the best alternative, statmech.mode isn't in the first list of places I'd look for this in.

alongd · 2019-04-30T18:50:32Z

arkane/statmech.py

+       write a .pes file for Q2DTor based on the
+       read in scans
+       """
+       atdict = {x.number:x.symbol for x in elementList}


You can use common.symbol_by_number instead

alongd · 2019-04-30T18:52:51Z

arkane/statmech.py

+# Calculations                     #
+#----------------------------------#
+start_calcs
+   level            hf 3-21g        # the calculation level


Level doesn't actually do anything in our implementation, right?

Nope, just a required part of the Q2DTor input file

alongd · 2019-04-30T18:53:18Z

arkane/statmech.py

+# Torsional PES                    #
+#----------------------------------#
+start_pes
+   t1step           10.0            # step in phi1 for scan calculation [degrees]


What if the user used a different step size?

It's related to Q2DTor launching jobs, I automatically write the pes file so it doesn't matter.

alongd · 2019-04-30T18:54:08Z

arkane/statmech.py

+# Working temperatures             #
+#----------------------------------#
+start_temperatures                 #
+   100.0   150.0   200.0          #


What if the user cares about a different T range?

The temperature range is unimportant because it's only used by Q2DTor after you get the eigenvalues, I just take the eigenvalues and calculate everything ourselves once we have them.

alongd · 2019-05-01T18:37:45Z

arkane/statmech.py

+       reads an available .evals file to get the QM energy levels
+       for the 2D-NS rotors
+       """
+       f = open(os.path.join(self.q2dtor_path,'IOfiles',self.name+'.evals'),'rU')


I think open(... 'U') is deprecated, take a look

mjohnson541 · 2019-07-30T18:09:15Z

replaced by Multidimensional rotors

mjohnson541 self-assigned this Apr 24, 2019

mjohnson541 added Arkane Complexity: Medium Status: Ready for Review PR is complete and ready to be reviewed Type: Feature labels Apr 24, 2019

mjohnson541 requested a review from alongd April 24, 2019 22:39

mjohnson541 force-pushed the q2dtor branch from 8827f06 to 6d55ea4 Compare April 24, 2019 22:43

mjohnson541 added 14 commits April 29, 2019 11:38

allow degrees of freedom to be supplied by a dof attribute on a Mode …

d0cf148

…object

switch arkane/statmech.py from import numpy to import numpy as np

cb61ada

create HinderedRotor2D object with appropriate attributes

d89d3a6

calcPath is the a directory containing rotor calculations named: scangeom_{name}_{phi1}_{phi2}.out and input files scangeom_{name}_{phi1}_{phi2}.gjf automatically constructs a directory based on self.name to run Q2DTor in

add function for reading energies, coordinates and angles from scan f…

ba9e317

…iles

add functions for determining dihedrals for q2dtor input file

3feee80

add functions for writing q2dtor input files

7cefd85

add functions for calling q2dtor on the input files to generate appro…

c469f9a

…priate files

add functionality for reading the energy levels from the q2dtor .eval…

69986fe

…s file

add functions for computing statistical mechanical properties based o…

7d5879a

…n the energy levels of the 2D-NS partition function

add a single function for calculating the energy levels of the 2D-NS …

765eccb

…rotors so that statmech properties can be calculated

add HinderedRotor2D to rotor processing

610fa58

count HinderedRotor2D as two rotors in projectRotors

df50a37

adjust rotor processing to project out both rotors from HinderedRotor2D

c1f723b

add example using 2D-NS rotors

76a56ed

mjohnson541 force-pushed the q2dtor branch from 98b1a33 to 76a56ed Compare April 29, 2019 15:39

mjohnson541 removed the Complexity: Medium label Apr 30, 2019

alongd reviewed May 1, 2019

View reviewed changes

mliu49 mentioned this pull request May 29, 2019

Use the QC partition function by default in Torsion #1609

Closed

alongd mentioned this pull request Jul 29, 2019

Multi-Dimensional Rotors #1640

Merged

mjohnson541 closed this Jul 30, 2019

Conversation

mjohnson541 commented Apr 24, 2019

Uh oh!

codecov bot commented Apr 29, 2019 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

alongd left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

mjohnson541 commented Jul 30, 2019

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

codecov bot commented Apr 29, 2019 •

edited

Loading