Bugs with running coordinate scans
Posted: Fri Aug 07, 2020 1:52 am
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.
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
which is probably inadvertently getting interpretted by parse_nwchem.cgi, resulting in the output table having two erroneous rows before the actual data:
Forth, MOPAC 2016 seems to work just fine for coordinate scans (1D and 2D).
Niko Loening
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.
Code: Select all
%geom
invertConstraints true
Scan
B 1 0 = 0.40 , 1.50 , 15
end
end
Code: Select all
if (ga_nodeid() == 0): print ' x = %5.2f x2 = %5.2f energy = %10.6f' % (x, x2, energy)
Code: Select all
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
...
Niko Loening
Code: Select all
-----------------------------------------------------------------------
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
https://github.com/psi4/psi4/blob/master/codemeta.json
https://github.com/psi4/psi4/graphs/contributors
http://psicode.org/psi4manual/master/introduction.html#citing-psifour
-----------------------------------------------------------------------
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
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')
print_out(str(result_table))
--------------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/miniconda/bin/psi4", line 337, in <module>
exec(content)
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>
exec(content)
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