Bugs with running coordinate scans

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Posts: 4
Joined: Fri Aug 07, 2020 1:27 am
Full Name: Nikolaus Loening
Organization: Lewis & Clark College
Subdiscipline: Chemistry

Bugs with running coordinate scans

Post by loening »

So, I’ve been playing around with coordinate scans and have run into a few bugs with 1D and 2D scans.

First, Psi4 always fails when doing a coordinate scan with the output copied at the end of this post.

Second, ORCA4 can do 1D scans, but attempts to run a 2D scan just end up producing a 1D coordinate scan (i.e., the second coordinate seems to get ignored). I can see that input.inp file only scans one coordinate, so the problem must be in how WebMO generates input.inp.

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invertConstraints true
B 1 0 = 0.40 , 1.50 , 15 
Third, NWChem works fine for 1D scans. 2D scans will complete, but the output has a couple rows of string formatting code in the output that prevents graphing. I can manually remove these first two “data points” from the output.properties file in the job directory, in which case the output will graph correctly. There are a couple of sections of python code in the NWChem output that have the string formatting text

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if (ga_nodeid() == 0): print ' x = %5.2f x2 = %5.2f energy = %10.6f' % (x, x2, energy)
which is probably inadvertently getting interpretted by parse_nwchem.cgi, resulting in the output table having two erroneous rows before the actual data:

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Coordinate 1     Coordinate 2    Energy
 %5.2f	%5.2f	%10.6f'	 
%5.2f	%5.2f	%10.6f'	 
0.40	0.40	-0.802124	 
0.40	0.42	-0.834106	 
Forth, MOPAC 2016 seems to work just fine for coordinate scans (1D and 2D).

Niko Loening

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          Psi4: An Open-Source Ab Initio Electronic Structure Package
                               Psi4 1.4a2.dev723 

                         Git: Rev {master} fb499f4 

    D. G. A. Smith, L. A. Burns, A. C. Simmonett, R. M. Parrish,
    M. C. Schieber, R. Galvelis, P. Kraus, H. Kruse, R. Di Remigio,
    A. Alenaizan, A. M. James, S. Lehtola, J. P. Misiewicz, M. Scheurer,
    R. A. Shaw, J. B. Schriber, Y. Xie, Z. L. Glick, D. A. Sirianni,
    J. S. O'Brien, J. M. Waldrop, A. Kumar, E. G. Hohenstein,
    B. P. Pritchard, B. R. Brooks, H. F. Schaefer III, A. Yu. Sokolov,
    K. Patkowski, A. E. DePrince III, U. Bozkaya, R. A. King,
    F. A. Evangelista, J. M. Turney, T. D. Crawford, C. D. Sherrill,
    J. Chem. Phys. 152(18) 184108 (2020). https://doi.org/10.1063/5.0006002

                            Additional Code Authors
    E. T. Seidl, C. L. Janssen, E. F. Valeev, M. L. Leininger,
    J. F. Gonthier, R. M. Richard, H. R. McAlexander, M. Saitow, X. Wang,
    P. Verma, and M. H. Lechner

             Previous Authors, Complete List of Code Contributors,
                       and Citations for Specific Modules


    Psi4 started on: Thursday, 06 August 2020 06:14PM

    Process ID: 31958
    Host:       spin
    PSIDATADIR: /usr/local/miniconda/share/psi4
    Memory:     500.0 MiB
    Threads:    4
  ==> Input File <==

memory 1024 mb

molecule webmoMolecule{
0 1
N 1 B1

B1= 0.500000000


set scf_type df
set basis 6-31G(d)
set reference rhf

s1vals = [x*0.166666666666667+0.5 for x in range(int(round(abs(2-0.5)/0.166666666666667))+1)]
result_table = Table(rows=("Values"),cols=("Energies"))
for value in s1vals:
  webmoMolecule. = value
  result_table[value] = energy('scf')

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/psi4", line 337, in <module>

  File "<string>", line 33
    webmoMolecule. = value
SyntaxError: invalid syntax

    Psi4 stopped on: Thursday, 06 August 2020 06:14PM
    Psi4 wall time for execution: 0:00:00.00

*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at github.com/psi4/psi4.
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/psi4", line 337, in <module>
  File "<string>", line 33
    webmoMolecule. = value
SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/psi4", line 354, in <module>
    suspect_lineno = traceback.extract_tb(exc_traceback)[1].lineno - 1  # -1 for 0 indexing
IndexError: list index out of range

Posts: 35
Joined: Sat May 30, 2020 3:00 pm
Full Name: JR Schmidt
Organization: WebMO, LLC

Re: Bugs with running coordinate scans

Post by schmidt »

Thanks for these reports. I'm not sure what is happening with Orca. The PSI4 and NWChem issues are probably related to Python changes, since in many cases the codes have changed from Python 2->3 in the last few years -- and both are moving targets in terms of output changes, etc. I'll address these in the next bugfix release.

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