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input_grrm_advv

esta.gaussianBag.input_grrm_advv

GenerateCom

python class to generate input files (*.com file) for different type of calculations for GRRM using:

  • non-supported

  • orca

  • gaussian

.. note:: Different types of calculation are carried out by the 

GRRM software given below:


     calculaiton type                          .... status of Implementation
===============================================================================
1)
   - Normal mode analysis (FREQ)
   - Minimum point optimization (MIN)          ......DONE
   - Saddle-point optimization (SADDLE)
   - IRC following (IRC)
   - LUP path optimization (LUP)               .... ongoing

   -- to do 
    Crossing point (MECI or MESX) optimization ....  will not be done
    Crossing point (MECI or MESX) estimation   ....     will not be done
    External atoms (microiterations)
    Frozen atoms                               .... DONE

2)

   MIN-AFIR calculations                      ...  DONE
   AFIR calculations                          ...  DONE
   DS-AFIR calculations                       ...  DONE

   Refinement calculations                    ..... TODO

author: skumar email: sonukumar.physics@gmail.com

read_xyz()

Parameters

filename : str xyz file name

Returns

atomic positions : array rank 2 array of shape (natoms, 3) atomic labels : list/array of strings rank 1 array of atomic labels strings : string string mentioning the units of coordinates

read_xyz2(xyz2file)

Returns:

  • atomic positions: array: rank 2 array of shape (natoms, 3) –

    atomic labels: list/array of strings: rank 1 array of atomic labels no of atoms: scalar

flags_grrm(**kwargs)

options in GRRM code for calculation types

.. note::

Options
sublink=/home/kumarsonu/bin/link_excode_allv3.1_.py
Add Interaction
Fragm.1=56,57,58,1
Fragm.2=59-62
1 2
Gamma=200.0
END
NOFC
KeepIntFiles
DownDC=12

write_com(interface=None, basis=None, solvent=None, log_filename=None, **kwargs)

input: 
atomic postions
atomic labels
no of atoms
kwargs containing GRRM related parameters
output: 
input com GRRM file containing info of atomic structure as well 
as other GRRM parameteres

write_com_2xyz(xyz2file, interface=None, **kwargs)

xyz files of products read from command line arguments ....mainly used for creating DS-AFIR input file ...

input: 
atomic postions
atomic labels
no of atoms
_________________ --> all of these variable read form 1xyz file ..by 
                        calling self.read_xyz()

str: xyz file name ---2nd xyz filename correspinding to product of rxn
output: 
com file containing info of atomic structure info of two atomic systems

write_inp(xyzfile, charge, multiplicity, ncores=None, memory=None, interface=None)

generate input file for ORCA like below:

Parameters:

  • prefix –

    name of inp file with .inp extension

  • charge –

    chare on ths system

  • multiplicity –

    spin multiplicity (2S+1); for a single electron: S =½

Returns:

  • file ( string ) –

    inp file for orca containg charge and multiplicity options

  • .. note:: –

    ! XTB2 NoUseSym @job

write_input_oniom()

get input file for the oniom-msm method by suzuki etal. (ICReDD) for:

  • saddle calculations (see general folder for the implementation)
  • EQ/TS sampling calculations (this may not be possible as I tried setting up the calculation, but failed!!)
  • ReStruct calculation ..