Parse empirical dispersion corrections by berquist · Pull Request #745 · cclib/cclib

berquist · 2019-05-26T05:39:13Z

Extends #418 to all parsers. Closes #660. Closes #664.

berquist · 2020-02-17T21:08:10Z

Comment to myself: this is still draft while the following issues exist

********* SUMMARY OF ERRORS *********

basicPsi4-1.2.1/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 400, in testdispersionenergies
    self.assertTrue(len(self.data.dispersionenergies), 1)
  File "/home/eric/development/cclib_berquist/test/test_data.py", line 124, in ccdata_getattribute_with_coverage
    return object.__getattribute__(self, attr)
AttributeError: 'ccData' object has no attribute 'dispersionenergies'


********* SUMMARY OF FAILURES *********

basicFirefly8.1/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 401, in testdispersionenergies
    self.assertAlmostEquals(self.data.dispersionenergies[0], -0.40407836521053214)
AssertionError: -0.42998210046822655 != -0.40407836521053214 within 7 places (0.025903735257694405 difference)

basicGAMESS-US2018/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 401, in testdispersionenergies
    self.assertAlmostEquals(self.data.dispersionenergies[0], -0.40407836521053214)
AssertionError: -0.40054977293661714 != -0.40407836521053214 within 7 places (0.003528592273914999 difference)

basicGaussian16/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 401, in testdispersionenergies
    self.assertAlmostEquals(self.data.dispersionenergies[0], -0.40407836521053214)
AssertionError: -0.40054946000568914 != -0.40407836521053214 within 7 places (0.0035289052048430025 difference)

basicNWChem6.8/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 401, in testdispersionenergies
    self.assertAlmostEquals(self.data.dispersionenergies[0], -0.40407836521053214)
AssertionError: -0.4005497099422608 != -0.40407836521053214 within 7 places (0.0035286552682713412 difference)

basicORCA4.1/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 401, in testdispersionenergies
    self.assertAlmostEquals(self.data.dispersionenergies[0], -0.40407836521053214)
AssertionError: -0.4005497375618166 != -0.40407836521053214 within 7 places (0.003528627648715532 difference)

basicQChem5.1/dvb_dispersion_bp86_d3zero.out: None
testdispersionenergies (test.data.testSP.GenericDispersionTest)Traceback (most recent call last):
  File "/home/eric/development/cclib_berquist/test/data/testSP.py", line 401, in testdispersionenergies
    self.assertAlmostEquals(self.data.dispersionenergies[0], -0.40407836521053214)
AssertionError: -0.4005494953804897 != -0.40407836521053214 within 7 places (0.0035288698300424692 difference)

ghutchis · 2020-06-09T16:34:02Z

Is this a difference between D3 "zero" and D3BJ?

berquist · 2020-06-09T17:54:28Z

@ghutchis if I remember correctly, it's mostly that, but there may have been something else. I started switching from D3(0) to D3(BJ) since not all programs I have access to can do D3(0), strangely. I'll check tonight, also to make sure I don't have changes in a stash.

ghutchis · 2020-06-09T20:17:02Z

The Firefly example seems totally out of left field.. You can always check with dftd3 to get the 'authentic' numbers:
https://anaconda.org/psi4/dftd3

That's the Psi4 modified version, but IIRC Lori didn't change anything (https://github.com/loriab/dftd3)

berquist · 2020-06-10T04:00:10Z

Here's the current state of this PR. Some of these might just be stray untracked outputs in my work directories. All calculations using BP86.

program	version	D3 damping	energy
DALTON	2018	BJ	-0.89908282
DALTON	2018	zero	-0.40407837
Firefly	8.1	?	-0.4299821
GAMESS	2018	BJ	-0.90884967
GAMESS	2018	zero	-0.40054977
GAMESS	2018	?	-0.97852033
Gaussian	16	zero	-0.40054946
Molpro	2018	zero	`mocoeffs` parsing broken
NWChem	6.8	zero	-0.40054971
ORCA	4.0	?	-4.24985755
ORCA	4.1	zero	-0.40054974
Psi4	1.2.1	zero	can't parse yet?
Q-Chem	5.1	zero	-0.4005495

Filtered just for D3(0) and working,

program	version	energy
DALTON	2018	-0.40407837
Firefly	8.1	-0.4299821
GAMESS	2018	-0.40054977
Gaussian	16	-0.40054946
NWChem	6.8	-0.40054971
ORCA	4.1	-0.40054974
Q-Chem	5.1	-0.4005495

It looks like the next reasonable tasks are:

Get BP86/D3(0) corrections for the geometries in the DALTON and Firefly inputs.
- If dftd3 is consistent with DALTON and Firefly, then the geometries are different; update the geometries and rerun. Consistent geometries is already a known issue: Using standardized inputs for testing #407
- If dftd3 is consistent with every other package, then there is something up with the Firefly and DALTON settings or implementations; make specific unit tests and link to this comment.
Run the ORCA 4.2 calculation.
Implement for Psi4.

Anything for Molpro will have to wait until #872 is done, which will take more time.

berquist · 2020-06-10T04:28:56Z

The Q-Chem and Firefly results with dftd3 are identical, but comparing against the DALTON geometry:

program's input geometry	energy (a.u.)	energy (eV) using cclib converter
Q-Chem	-0.01471993	-0.40054968313904654
DALTON	-0.01484961	-0.40407845555233046

This indicates that

the geometries we use with DALTON are inconsistent, and
something else is going on with Firefly.

berquist · 2020-06-11T02:58:18Z

I've updated the geometry for the DALTON calculation and now the results are identical. To take a look at the raw outputs, we can see that at least part of the Firefly parameters are different from DALTON and Q-Chem:

param	DALTON	Q-Chem	Firefly
s6	1.000	1.000	1.000
s8	1.683	1.683	1.682
sr6	1.139	1.139	1.094
sr8	1.000	1.000	1.000
alpha	14.000	?	?
k1	?	?	16
k2	?	?	1.333
k3	?	?	-4
rthr			20000
rthr2	?	?	1600

The nuclear repulsion energy is also wrong, even before adding the dispersion correction.

DALTON:

                      DFT-D Empirical Dispersion Correction
                      -------------------------------------

       Running DFT-D Version :     3
                   Reference : S. Grimme, J. Antony, S. Ehrlich and H. Krieg, 
                               J. Chem. Phys. 132 (2010), 154104
       Becke-Johnson Damping :    F
                3-body terms :    F


                      DFT-D3 Functional Dependent Parameters
                      --------------------------------------

      s_6 =       1.000000000000     sr_6 =       1.139000000000
      s_8 =       1.683000000000     sr_8 =       1.000000000000
      alp =      14.000000000000


                          +------------------------------+
                          ! Dispersion Energy Correction !
                          +------------------------------+

                      E_disp :         -0.014719923805

Q-Chem:

 Adding empirical dispersion correction 
 ----------------------------------------------------------------
 Doing -D3(0) with
 s6  =   1.00000
 s8  =   1.68300
 rs6 =   1.13900
 rs8 =   1.00000
 -D3 energy without 3body term =     -0.0147199231 hartrees

Firefly:

Loading Firefly/DFT-D extension... loaded successfully (version  1.0001).

 Firefly/DFT-D extension capabilities:
 Minimum supported DFT-D version is   2
 Maximum supported DFT-D version is   4
 For DFT-D version   2, max supported atomic no. is  86
 For DFT-D version   3, max supported atomic no. is  94
 For DFT-D version   4, max supported atomic no. is  94

 Using DFT-D version  3
 Cite DFT-D3 as:
 S. Grimme, J. Antony, S. Ehrlich and H. Krieg,
 J. Chem. Phys. 132 (2010), 154104

 Initializing DFT-D extension... initialized successfully!

     ---------------------------------------------
         Parameters controlling DFT-D run are:
     ---------------------------------------------
     VERSN =             3   S6    = 1.0000000E+00
     RS6   = 1.0940000E+00   S18   = 1.6820000E+00
     RS18  = 1.0000000E+00   ALP   = 1.4000000E+01
     K1    = 1.6000000E+01   K2    = 1.3333333E+00
     K3    =-4.0000000E+00   RTHR  = 2.0000000E+04
     RTHR2 = 1.6000000E+03   NUMGRD=             F
     ABC   =             F   TZ    =             F

berquist · 2020-06-29T14:04:32Z

Molpro is implemented, but not tested, since there are bigger problems with parsing MO coefficients from the latest version (#872).

shivupa · 2020-08-03T03:41:48Z

Sorry for the delay. This looks good to me, and I'm in favor of merging. I just have a question:

The nuclear repulsion energy is also wrong, even before adding the dispersion correction.
The firefly nuclear repulsion energy? Can this and the difference in parameters be reported upstream?

shivupa · 2020-08-03T03:44:02Z

cclib/parser/orcaparser.py

+            # However, they vary wildly in form and number, making parsing problematic
+            line = next(inputfile)
+            while 'Dispersion correction' not in line:
+                line = next(inputfile)


Should we do self.skip_lines(inputfile,["Dispersion parameters"])

It isn't clear if the number of lines to skip is fixed, and we (I?) do this in other places.

langner

I think there's some details to fill in here. But given the magnitude of this change, I think Shiv is right and I'm going to merge. We can clean up anything that's left later.

berquist · 2020-08-05T02:50:45Z

Can this and the difference in parameters be reported upstream?

I see in the 8.2.0 (latest version) changelog

Changes to use newer, more precise value of Bohr radius, namely
0.52917721067 Angstrom, throughout all the code. Previous versions
of Firefly used older, less precise value of 0.52917724924 Angstrom.
Note: this transition causes minor differences in computed energies and
other properties as compared to older Firefly versions when initial
geometry is specified using Angstroms.

which may account for this (I used 8.1.1). It's possible that 8.2.0 has fixed this. I have the 8.2.0 archive, but never registered it to get the password.

berquist · 2020-08-05T03:32:33Z

I think there's some details to fill in here.

I can't think of anything off the top of my head. What do you think is missing?

berquist added feature parsers ORCA labels May 26, 2019

berquist added this to the v1.6.2 milestone May 26, 2019

langner modified the milestones: v1.6.2, v1.6.3 Sep 5, 2019

berquist force-pushed the 664-dispersion branch from 62e4160 to fced82d Compare December 10, 2019 05:05

berquist force-pushed the 664-dispersion branch 2 times, most recently from d4119fd to c5d2959 Compare February 17, 2020 21:05

berquist mentioned this pull request Apr 7, 2020

Parses ORCA dispersion correction #418

Closed

berquist mentioned this pull request Apr 29, 2020

Parse intrinsic reaction coordinate calculations from ORCA #842

Open

langner modified the milestones: v1.6.3, v1.6.4 May 2, 2020

berquist mentioned this pull request Jun 9, 2020

Ensure dispersion correction is added to scfenergies for all packages #664

Closed

14 tasks

jevandezande and others added 5 commits June 9, 2020 23:17

Adds dispersion correction.

53186f2

Add dispersion unit tests for most packages

9557fce

Check length of dispersion energies

db92337

ORCA: add dispersion energy to SCF energy

df1d037

QChem: parse dispersion energy

3561162

Dispersion: use better reference value

9850a97

berquist force-pushed the 664-dispersion branch from c5d2959 to 9850a97 Compare June 10, 2020 04:43

DALTON: update dispersion unit tests with Q-Chem geometry

fe44157

berquist changed the title ~~[WIP] Parse empirical dispersion corrections~~ Parse empirical dispersion corrections Jun 11, 2020

berquist added 14 commits June 10, 2020 23:04

Firefly: use customized dispersion unit test

bcf9307

Psi4: fix reading dispersion correction

958a60f

Psi4: update geometry for dispersion calculation

3dc836c

ORCA: remove unused dispersion energy unittest files

c77c80d

ORCA: copy dispersion unittest from 4.1 to 4.2

9a21396

ORCA: update real 4.2 dispersion unittest file

b30e4ea

Psi4: copy dispersion unittest from 1.2.1 to 1.3.1

696ba77

Psi4: update real 1.3.1 dispersion unittest file

1c18165

Dispersion: enable unittest for ORCA 4.2

450e981

Dispersion: enable unittest for Psi4 1.3.1

40c5e0d

Dispersion: remove unused Molpro 2018 unittest line

b3b5100

Gaussian: copy dispersion unittest from 16 to 09

0ea199a

Gaussian: update real 09 dispersion unittest file

641369b

Dispersion: enable unittest for Gaussian 09

d09de00

berquist marked this pull request as ready for review June 29, 2020 13:58

berquist requested review from langner and shivupa June 29, 2020 13:59

shivupa approved these changes Aug 3, 2020

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shivupa reviewed Aug 3, 2020

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langner approved these changes Aug 3, 2020

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langner merged commit 027d462 into cclib:master Aug 3, 2020

berquist deleted the 664-dispersion branch August 5, 2020 01:27

berquist mentioned this pull request Apr 24, 2023

No SCF correction read from ORCA logfiles (dispersion, gCP, correlation from coupled cluster methods, etc.) #806

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berquist commented May 26, 2019

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