Create a .cube file of the molecular electrostatic potential using ORCA.

mep.py

"""
(c) 2013, 2019, 2022 Marius Retegan
License: BSD-2-Clause
Description: Create a .cube file of the molecular electrostatic
             potential (MEP) using ORCA.
Run: python mep.py basename npoints nprocs (e.g. python mep.py water 40 2).
Arguments: basename - file name without the extension;
                      this should be the same for the .gbw and .scfp.
           npoints  - number of grid points per side
                      (80 should be fine)
           nprocs - number of processors for parallel calculations
"""

#!/usr/bin/env python


def read_xyz(xyz):
    atoms = []
    x, y, z = [], [], []

    with open(xyz) as fp:
        # Skip the first two lines.
        next(fp)
        next(fp)
        for line in fp:
            data = line.split()
            atoms.append(data[0])
            x.append(float(data[1]))
            y.append(float(data[2]))
            z.append(float(data[3]))

    return atoms, np.array(x), np.array(y), np.array(z)


def read_vpot(vpot):
    v = []

    with open(vpot) as fp:
        next(fp)
        for line in fp:
            data = line.split()
            v.append(float(data[3]))

    return np.array(v)


if __name__ == "__main__":
    import os
    import shutil
    import subprocess
    import sys

    import numpy as np

    ang_to_au = 1.0 / 0.5291772083


    elements = [None,
         "H", "He",
         "Li", "Be",
         "B", "C", "N", "O", "F", "Ne",
         "Na", "Mg",
         "Al", "Si", "P", "S", "Cl", "Ar",
         "K", "Ca",
         "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
         "Ga", "Ge", "As", "Se", "Br", "Kr",
         "Rb", "Sr",
         "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd",
         "In", "Sn", "Sb", "Te", "I", "Xe",
         "Cs", "Ba",
         "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb",
         "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg",
         "Tl", "Pb", "Bi", "Po", "At", "Rn",
         "Fr", "Ra",
         "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No",
         "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Uub"]


    basename = sys.argv[1]
    xyz = f"{basename}.xyz"

    if not os.path.isfile(xyz):
        sys.exit("Could not find the .xyz. To quickly generate one for "
                 f"your molecule run: echo 11 | orca_plot {basename}.gbw -i.")

    atoms, x, y, z = read_xyz(xyz)

    try:
        npoints = int(sys.argv[2])
    except ValueError:
        sys.exit(f"Invalid number of points: {sys.argv[2]}")

    try:
        nprocs = int(sys.argv[3])
    except IndexError:
        nprocs = 1
    except ValueError:
        sys.exit(f"Invalid number of cpus: {sys.argv[3]}")

    natoms = len(atoms)

    extent = 7.0
    xmin = x.min() * ang_to_au - extent
    xmax = x.max() * ang_to_au + extent
    ymin = y.min() * ang_to_au - extent
    ymax = y.max() * ang_to_au + extent
    zmin = z.min() * ang_to_au - extent
    zmax = z.max() * ang_to_au + extent

    with open(f"{basename}_mep.inp", "w") as fp:
        fp.write(f"{nprocs:d}\n")
        fp.write(f"{basename}.gbw\n")
        fp.write(f"{basename}.scfp\n")
        fp.write(f"{basename}_mep.xyz\n")
        fp.write(f"{basename}_mep.out\n")

    with open(f"{basename}_mep.xyz", "w") as fp:
        fp.write(f"{npoints**3:d}\n")
        for ix in np.linspace(xmin, xmax, npoints, True):
            for iy in np.linspace(ymin, ymax, npoints, True):
                for iz in np.linspace(zmin, zmax, npoints, True):
                    fp.write(f"{ix:12.6f} {iy:12.6f} {iz:12.6f}\n")

    orca_vpot = shutil.which("orca_vpot")
    if orca_vpot is None:
        sys.exit(f"Could not find the orca_vpot executable.")

    subprocess.check_call(["orca_vpot", f"{basename}_mep.inp"])

    vpot = read_vpot(f"{basename}_mep.out")

    with open(f"{basename}_mep.cube", "w") as fp:
        fp.write("Generated with ORCA\n")
        fp.write(f"Electrostatic potential for {basename}\n")
        fp.write(f"{len(atoms):5d}{xmin:12.6f}{ymin:12.6f}{zmin:12.6f}\n")
        
        xstep = (xmax - xmin) / float(npoints - 1)
        fp.write(f"{npoints:5d}{xstep:12.6f}{0:12.6f}{0:12.6f}\n")
        
        ystep = (ymax - ymin) / float(npoints - 1)
        fp.write(f"{npoints:5d}{0:12.6f}{ystep:12.6f}{0:12.6f}\n")
        
        zstep = (zmax - zmin) / float(npoints - 1)
        fp.write(f"{npoints:5d}{0:12.6f}{0:12.6f}{zstep:12.6f}\n")

        for i, atom in enumerate(atoms):
            index = elements.index(atom)
            xi, yi, zi = x[i] * ang_to_au, y[i] * ang_to_au, z[i] * ang_to_au
            fp.write(f"{index:5d}{0:12.6f}{xi:12.6f}{yi:12.6f}{zi:12.6f}\n")

        m = 0
        n = 0
        vpot = np.reshape(vpot, (npoints, npoints, npoints))
        for ix in range(npoints):
            for iy in range(npoints):
                for iz in range(npoints):
                    fp.write(f"{vpot[ix][iy][iz]:14.5e}")
                    m += 1
                    n += 1
                    if (n > 5):
                        fp.write("\n")
                        n = 0
                if n != 0:
                    fp.write("\n")
                    n = 0

water.inp

# ORCA input file used to generate the files needed for the MEP calculation.
! bp86 def2-svp keepdens xyzfile

* xyz 0 1
O          0.00000        0.00000        0.11779
H          0.00000        0.75545       -0.47116
H          0.00000       -0.75545       -0.47116
*

@AJ2397 If you want to quantitatively analyze the MESP, then I would recommend you use Multiwfn (free). You can convert ORCA gbw files to molden files which can then be read into Multiwfn, which will compute the MESP and provide statistical analysis of the surface automatically. It also allows you to compute the MESP at specific points, among other things. Conveniently, all of this is covered in the extensive tutorials provided by the developer. Highly recommended, just make sure to use the “developer” version as the “official” version is very old and not as efficient. I cannot comment on the relative efficiency of it versus this Python script, though, but it is definitely more flexible. I also think you can hook it up to ORCA to compute the MESP more efficiently, but you’ll have to read the forums to get that working.

…

On Thu, Feb 15, 2024 at 9:51 AM ssarix ***@***.***> wrote: ***@***.**** commented on this gist. ------------------------------ @AJ2397 <https://github.com/AJ2397> I did not quite understand what are you trying to achieve. What is the error code that you encounter ? — Reply to this email directly, view it on GitHub <https://gist.github.com/mretegan/5501553#gistcomment-4903032> or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABA73NKBQCZCVYLAUHBRGJ3YTYOGZBFKMF2HI4TJMJ2XIZLTSKBKK5TBNR2WLJDUOJ2WLJDOMFWWLO3UNBZGKYLEL5YGC4TUNFRWS4DBNZ2F6YLDORUXM2LUPGBKK5TBNR2WLJDHNFZXJJDOMFWWLK3UNBZGKYLEL52HS4DFVRZXKYTKMVRXIX3UPFYGLK2HNFZXIQ3PNVWWK3TUUZ2G64DJMNZZDAVEOR4XAZNEM5UXG5FFOZQWY5LFU42TKMBRGU2THJ3UOJUWOZ3FOKTGG4TFMF2GK> . You are receiving this email because you commented on the thread. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> .