Examples¶

pyssian examples¶

Table of Contents

GaussianOutFile
GaussianInFile
Cube
LinkJob
Usage Examples

GaussianOutFile¶

pyssian.GaussianOutFile can be opened as a file object. When reading an already finished calculation file it is recommended to use the with statement as in this first example. If the file is being written the recommended way to open the file is as example 2 or 3.

from pyssian import GaussianOutFile
# Example 1
with GaussianOutFile(FilePath) as GOF1:
   GOF1.read()
# Example 2
GOF2 = GaussianOutFile(FilePath)
GOF2.read()
GOF2.close()
# Example 3
File = open(FilePath,'r')
GOF3 = GaussianOutFile(File)
GOF3.read()
File.close()

It also accepts another parameter that indicates which Links are of interest. The default behaviour (without specifying any value) is to consider all links.

A second option, only used to see the structure of the file without actually storing any information of each link is to pass -1 as the first value:

File = open(FilePath,'r')
with GaussianOutFile(File,parselist=[-1,]) as GOF:
    GOF.update(clean=False) # read is an alias for update(clean=True)

If you specify the numbers of the links to the GOF only those will be parsed and will not be cleaned afterwards.

File = open(FilePath,'r')
with GaussianOutFile(File,[1,103,202,502,9999]) as GOF:
    GOF.read()

GaussianInFile¶

pyssian.GaussianInFile can be instantiated either from an existing input file or to create a new file.

Note

Currently it is in an early stage as proper support for method-basis management as well as oniom and zmatrix support require special attention.

The following Code snippet shows how to create a new input from an existing one changing the geometry and method but retaining the rest of the options

from pyssian import GaussianInFile

initial_theory_file = 'InitialTheory.in'
initial_geometry_file = 'InitialGeometry.in'
output_file = 'Output.in'
with GaussianInFile(initial_theory_file) as theory_file:
    theory_file.read()
with GaussianInFile(initial_geometry_file) as geometry_file:
    geometry_file.read()
old_geometry = theory_file.geometry # In case we want to use it somewhere else
theory_file.geometry = geometry_file.geometry
theory_file.method = 'b3lyp'
with open(output_file,'w') as F:
    theory_file.write(F)

It combines fairly well with pyssian.classutils.Geometry to create inputs from outputs. The following code snippet is an example of how to create an input to continue an optimization that failed due to exceeding the number of optimization steps.

from pyssian import GaussianInFile, GaussianOutFile
from pyssian.classutils import Geometry

with GaussianOutFile('Old_Calc.out') as GOF:
   GOF.read()

# Get the last geometry of the calculation
geom = Geometry.from_l202(GOF.get_links(202)[-1])

# Get the Link1 of the GaussianOutFile
Link1 = GOF.get_links(1)[0]

# Extract the calculation type and commands
commandline = Link1.commandline
nprocs = Link1.nprocs
mem = Link1.mem
Link0 = Link1.link0

# Get Charge and spin from Link101
Link101 = GOF.get_links(101)[0]
charge = Link101.charge
spin = Link101.spin

# Now write the new input file
with GaussianInFile('New_Calc.in') as GIF:
    GIF.parse_commandline([commandline,])
    # We can instead set a dict for the variable GIF.commandline
    # "GIF.commandline = {'opt':'','freq':'NoRamman','b3lyp':''}"
    # but using parse_commandline is easier in this case.
    GIF.preprocessing = {key:'' for key in Link0}
    GIF.preprocessing['nprocshared'] = nprocs
    GIF.preprocessing['mem'] = mem
    GIF.title = 'New Title'
    GIF.spin = spin
    GIF.charge = charge
    GIF.geometry = geom
    GIF.write()

Cube¶

pyssian.classutils.Cube class was introduce to simplify the sometimes a bit bothersome usage of cubeman from gaussian to add, substract, multiply... cube files. You can initialize an empty cube and populate it yourself but the class was thought to be used as follows:

from pyssian.classutils import Cube
MO_1 = Cube.from_file('MO_01.cube')
MO_2 = Cube.from_file('MO_02.cube')
MO_3 = Cube.from_file('MO_03.cube')
FinalCube = MO_1*2 + MO_2 - MO_3**2
FinalCube.write('Final.cube')

LinkJob¶

The pyssian.LinkJob class is the base class for all the LinkJob subclasses And implements the two basic attributes of all Links, .number and .text. Currently the specific parsers implemented are:

Link1
Link101
Link103
Link123
Link202
Link502
Link508
Link601
Link716
Link804
Link913
Link914

with GaussianOutFile(File) as GOF:
    GOF.read()
Link = GOF[0][RandomPosition]
# General Attributes of all LinkJob classes
print(Link.number)
print(Link.text)

Link1¶

# From the file Get the first Link1
Link1 = GOF.get_links(1)[0]
# Attributes of Link1
Link1.commandline
Link1.nprocs
Link1.mem
Link1.link0
Link1.IOps
Link1.info # Will be deprecated in the future

Link101 & Link103¶

Link101 = GOF.get_links(101)[0]
Link101.spin
Link101.charge

Link103 = GOF.get_links(103)[0]
Link103.mode
Link103.state
Link103.conversion
Link103.parameters
Link103.stepnumber
Link103.scanpoint
if Link103.mode == 'Iteration':
    Link103.print_convergence()

Link123¶

Link123 = GOF.get_links(123)[0]
Link123.orientation
Link123.step
Link123.direction
Link123.reactioncoord

Link202¶

Link202 = GOF[-1].get_links(202)[0]
Link202.orientation
Link202.DistanceMatrix
Link202.print_orientation()
Link202.get_atom_mapping()

Link502 & Link508¶

list_of_links = GOF.get_links(502,508)
energies = [link.energy for link in list_of_links if link.energy is not None]

Link601¶

Link601 = GOF[-1].get_links(601)[-1]
Link601.mulliken
Link601.mulliken_heavy

Link716¶

Link716 = GOF[-1].get_links(716)[-1]
Link716.mode
Link716.dipole
Link716.units
Link716.zeropoint
Link716.thermal_energy
Link716.enthalpy
Link716.gibbs
Link716.EContribs
Link716.IRSpectrum

Link804 & Link913¶

Link804 = GOF.get_links(804)[-1]
Link804.MP2
Link804.SpinComponents
scs_corr = Link804.get_SCScorr()
HF_energy = GOF.get_links(502)[-1].energy
scs_energy = HF_energy + scs_corr

Link913 = GOF.get_links(913)[-1]
Link913.MP4
Link913.CCSDT

Link914¶

Link914 = GOF.get_links(914)[-1]
for es in Link914.excitedstates:
    number, energy, wavelen, OStrength, s2, transitions = es
    for transition in transitions:
        donor = transition.donor
        acceptor = transition.acceptor
        contribution = transition.contribution
        print(f'{donor} -> {acceptor}     {contribution}')
# which can be done for the excited states 2,5,6:
Link914.print_excitedstates(2,5,6,show_transitions=True)

Usage Examples¶

Code snippet to extract the last potential energy and geometry

from pyssian import GaussianOutFile

MyFile = 'path-to-file'
with GaussianOutFile(MyFile) as GOF:
   GOF.read()

final_geometry = GOF.get_links(202)[-1].orientation
last_potential_energy = GOF.get_links(502)[-1]
print(last_potential_energy)
print(str(final_geometry))

Code snippet to display 'Filename HF MP2 MP2(SCS)'

from pyssian import GaussianOutFile

MyFile = 'path-to-file'
with GaussianOutFile(MyFile,[1,502,804]) as GOF:
   GOF.read()

HF = GOF.get_links(502)[-1].energy
Link804 = GOF.get_links(804)[-1]
MP2 = Link804.MP2
MP2scs = HF + Link804.get_SCScorr()
print(f'{MyFile}\t{HF}\t{MP2}\t{MP2scs}')

Code Snippet to follow a file being written by gaussian

from time import sleep

from pyssian import GaussianOutFile

GOF = GaussianOutFile(MyFile,[-1,])
GOF.update(clean=False)
print(GOF[-1][-1])
sleep(10)
GOF.update(clean=False)
print(GOF[-1][-1])
GOF.close()