Fast computation of electrostatic potential on grid

mat · June 15, 2019, 1:56pm

Hi everyone, I have a question concerning the computation of the electrostatic potential of an arbitrary density on numerical grid.
At the moment I am accomplishing the task using the following code (through the psi4 python API):
Dreal = Dtest.real
wfn_scf.oeprop.set_Da_ao(psi4.core.Matrix.from_array(Dreal))
wfn_scf.oeprop.compute()
Vvals_dt = wfn_scf.oeprop.Vvals()
the grid (grid.dat ) and the wfn_scf object has been previously generated by
(ene,wfn = psi4.prop(‘blyp’, properties=[‘GRID_ESP’], return_wfn=True)).
I have noticed that when oeprop.compute() is invoked the grid_esp.dat file is created. But the electrostatic potential is available through wfn_scf.oeprop.Vvals() and I don’t need to write it down in a file. So I was guessing if there is some trick to avoid the creation of grid_esp.dat and save some time.
Thanks in advance for you suggestions.
Matteo

tstrunk · June 16, 2019, 6:55pm

Hi there,

I split this code into the old “oeprop compute” way and an in-memory calculation without the esp.dat file, which I use for Resp charges.

http://www.psicode.org/psi4manual/master/api/psi4.core.ESPPropCalc.html

import psi4.core as p4c
myepc = p4c.ESPPropCalc(wfn)
psi4_matrix = p4c.Matrix.from_array(points)
esps_psi4 = np.array(myepc.compute_esp_over_grid_in_memory(psi4_matrix))

Let me know, if you need code, which is more verbose.

Best,
Timo

mat · June 16, 2019, 7:30pm

Timo, thank you so much. I can not figure out how I missed this manpage.

mdpoleto · April 30, 2024, 2:32am

Hi @tstrunk

I am really interested in extracting the electric field over a grid. Can I assume compute_field_over_grid_in_memory is what I am looking for?

And I a newbie in Psi4, so if you happen to have an example of such calculation, that would be great. Thank you!

tstrunk · May 2, 2024, 7:19am

Hi @mdpoleto,

yes, most probably you are looking for that. You can find an example inside the tests:

github.com

psi4/psi4/blob/master/tests/python/mints14/input.py

#! Check for correctness of ESP values. The ESP values are calculated using one or four threads
#! The one thread values are checked against the four thread values. The one thread values are 
#! also checked against the reference values (1 thread values computed, when generating this test).
#! Caution: The reference values are not obtained using an actual physical reference, but rather
#! generated by Psi4 at one point in time.

import psi4
import psi4.core as p4c
import numpy as np

psi4.set_output_file("output.dat", False)

#H2O with minimal basis
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")

psi4.set_options({"d_convergence": 1e-10})

This file has been truncated. show original

Best,
Timo

mdpoleto · May 2, 2024, 9:02pm

That is great, thank you very @tstrunk . Do you happen to know the unit in which the electric fields are output by compute_field_over_grid_in_memory?

system · July 1, 2024, 9:02pm

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