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Tutorials

This part of the project documentation focuses on examples usage of EStA.

  • Read xyz file data.

Example

#import esta.general.aadhaar as aadh  [this also works]
#aad = aadh.Aadhaar()

from esta import Xat # import Xat class
Xat.read_xyz(filename='x.xyz')
  • Substitution of atoms by other atom or gp of atoms.

Example

import glob
import esta.general.substitute_atom as substitute

atomid = 10
xyzfile = 'path_0000.xyz'
xyz_subs_file = 'methyl.xyz'  # taken from lib_xyz in esta

# atomid = 62
# xyzfile = 'de_SUB_path_all_all.xyz'
# xyz_subs_file = 'H.xyz' 

atom_id_subs = 1  #Generally.. C-atom Must be the first atom in the substituent 
part 

print('list of files: {}'.format(xyzfile))

substitute.substitute_atom_by_atoms(atomid=atomid, atom_id_subs=atom_id_subs,\
xyzfile=xyzfile, xyz_subs_file=xyz_subs_file)
  • Read poscar file data.

Example

import esta.vaspBag.inout.crystal_lattice as clatt
xlatt = clatt.Crystal_Lattice("POSCAR", ''./)
# or xlatt=clatt.CrystalLattice()
xlatt.read_poscar()
print('atomic positions: {}'.format(xlatt.tau_cartesian))
print('atomic positions in crystal coordinates: {}'.format(xlatt.tau_direct))

xlatt.get_cell_matrix
#array([[7.35205746, 0.        , 0.        ],
#       [3.67602873, 6.36706853, 0.        ],
#       [3.67602873, 2.12235618, 6.00292978]])

xlatt.get_cell_vectors
#(array([7.35205746, 0.        , 0.        ]),
# array([3.67602873, 6.36706853, 0.        ]),
# array([3.67602873, 2.12235618, 6.00292978]))

xlatt.LV1
#array([7.35205746, 0.        , 0.        ])

xlatt.LV3
#array([3.67602873, 2.12235618, 6.00292978])

xlatt.real_volume
#281.0034678144921 in A^3

# print each atom type
xlatt.get_each_atm_type
#[1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3]

# print no. of atoms of each type
xlatt.get_natm_type
#array([ 4,  4, 14])

*Similary other method of the xlatt object can be excessed; currently all available methods are:*
# 'atm_type', 'each_atm_type', 'filename', 'get_all_atoms_labels', 'get_atm_type', 'get_cell_matrix',
# 'get_cell_vectors', 'get_dispPOSCAR', 'get_each_atm_type', 'get_grouped_list', 'get_natm_type',
# 'get_neach_type', 'get_poscar', 'get_rVolume', 'get_reciprocal_lattice', 'get_selectivePOSCAR',
# 'get_unique_list', 'is_cartesian', 'is_crystal', 'is_selective_dynamics', 'l_SelectDynamics',
# 'l_crystal', 'location', 'natm_type', 'natoms', 'read_poscar', 'real_volume', 'reciprocal_lattice',
# 'tau_cartesian', 'tau_cartestain', 'tau_direct', 'to_cartesian', 'to_crystal'
  • Rename_files_using_index_for_ANY (collection of xyz or poscar files).

Example

import glob
import esta.general.rename_general as rename

#files = glob.glob("SUB_de_SUB*.xyz")
files = glob.glob("rlx*.xyz")

#--for keeping  part of the file--for example: [0,-2] part is kept ; last part is removed
first_index=False # if false mean 2nd index is also taken!
str_indx = [0,-2] #,[4,-2]] #  for first_index = False
#str_indx = [[0,-2] ,[4,-2]] #  ALSO can be used**

#--for removing begining part of the file--for example: [0,3]; this part is removed; last is kept
#first_index=True 
#str_indx = [0,3] #   for first index=True


for ifile in files:
    print('ifile is: {}'.format(ifile))
    rename.to_file_any(ifile, str_indx, first_indx_only=first_index, file_extension='xyz') #POSCAR' )
  • Create input file for the vasp calculations.

Example

import esta.vaspBag.vaspin as vaspin
vaspobj = vaspin.vasp()
vaspobj.get_vasp_input(poscar_name='POSCAR')
  • Create supercell from the input POSCAR

Example

from esta.general import operation as op
from esta import Xlat

poscar_files = glob.glob('*POSCAR')
for poscar_file in poscar_files:
    pos_obj = Xlat(poscar_file)
    obj = op.Transform(pos_obj)
    obj.get_supercell_([1,1,2])  # 1x1x2 Supercell creation 
    print('get sposcar:')
    obj.get_sposcar_('S_'+str(poscar_file))
  • Create POSCAR with selective tags

Example

import numpy as np
import glob
import esta.vaspBag.inout.crystal_lattice as clatt
import esta.general.aadhaar as aad
aad_obj = aad.Aadhaar()

filename= 'Ir111.vasp'
fix_atoms_list = ['1-8'] #,'30','8','29']
fix_direction = 'xyz' # 'z' # 'xy'

files = glob.glob(filename)
for posfile in files:
    xlatt = clatt.CrystalLattice(posfile)
    xlatt.read_poscar()
    pos=xlatt.tau_cartesian
    symb, _, _ = xlatt.get_all_atoms_labels()
    natom = xlatt.natoms
    lv1 = xlatt.LV1
    lv2 = xlatt.LV2
    lv3 = xlatt.LV3

    fle ="_".join( i for i in posfile.split("_")[0:-1]  ) + str('POSCAR')
    xlatt.get_selectivePOSCAR_adv(ldisp=True, disp_atoms_num=fix_atoms_list,\
                                  fix_direction=fix_direction, outfile='fix_'+str(fle))
  • Get forces, and poscar from the vasp xml

Example

import esta
from esta.vaspBag.inout import crystal_lattice as clatt
from esta.general import aadhaar 
from  esta.vaspBag.inout import xml_vasp_adv
import numpy as np

aad = aadhaar.Aadhaar()
print ("")
print ('***********************************************')
print ("reading forces from vasprun.xml file ...")

out_xmla = xml_vasp_adv.read_vasp_xml('vasprun.xml')
celll = out_xmla[0]
position_scaled = out_xmla[1]
symbol= out_xmla[2]
forces = out_xmla[-1]
print("forces are: ")


forc = []
for j in range(np.shape(forces)[0]):
     print(("{0:9.6f} {1:9.6f} {2:9.6f} {3:6.4f}".format( forces[j][0],\
        forces[j][1], forces[j][2], np.linalg.norm(forces[j]))))
     forc.append(np.linalg.norm(forces[j]))

print("Lattice vectors/Cell:")
print(celll)
print("positions in scaled coordinates:")
print(position_scaled)   
aad.get_poscar(out_xmla[0], out_xmla[1], out_xmla[2], 'vaspxml')
  • Read POSCARs for reactants and products in a reaction and generate intermediate structures.

Example

import numpy as np
from  esta.vaspBag.inout.crystal_lattice import CrystalLattice
import esta.general.get_configs as get_configs

output = CrystalLattice(filename = 'ach3oh_00_POSCAR', location = "./")
output.get_poscar()
atompositions = output.tau_cartesian

output2 = CrystalLattice(filename = 'cxyz_POSCAR', location = "./")
output2.get_poscar()
poscar_obj2 = output2 #.get_poscar()
atompositions2 = output2.tau_cartesian
N = 9
configurations = get_configs.get_atomic_configurations(N, atompositions, atompositions2)
print(configurations[1])

get_configs.get_poscar_images(N, poscar_obj, poscar_obj2)
  • Create qe input file for QE calculations with option 1*

Example

import glob
import esta.qeBag.gen_qeinput_advv as gen_qeinput

ps_info = ('pbesol', '_v1.*')

posfiles=glob.glob('*POSCAR')
for ifile in posfiles:
    gen_qeinput.get_qe_input(ifile, ps_info, lprint_cell ='angstrom',\
    cal_type='vc-relax', lcopy_pseudo=True, l_pseudo_GVRB=True)
  • Create qe input file for QE calculations with option2:

Example

import glob
import esta.qeBag.gen_qeinput_advv as gen_qeinput

#location = '~/pslibrary.1.0.0' 
ps_info = (
            # 'pbesol', '-*rrkjus_*',
            # 'pbesol', '-*kjpaw_*',
            'pbe', '-*kjpaw_*',
        )

cal_type = 'relax'
            # scf
            # vc-relax
poscar_files = '1POSCAR'

qe_parameters = \
{
    '&CONTROL': {   
    'calculation': cal_type,
    'restart_mode': 'from_scratch',
    'prefix': 'ir',
    'nstep': 400,
    'max_seconds': 386000,
    'pseudo_dir': './',
    'outdir': './tmp',
    'tstress': '.true.',
    'tprnfor': '.true.',
    'verbosity': 'low',
    },

 '&SYSTEM': {
    # 'ecutwfc': 60.0, 
    # 'ecutrho': 240.0,
    },

 '&ELECTRONS': {
    "electron_maxstep" : 400,
    #"conv_thr"         : '1.0d-8',
    "mixing_beta"      : 0.3,
    #"diagonalization"  :"cg",
    },

 '&IONS': {
    'ion_dynamics': 'bfgs'
    },

 '&CELL': {
    'cell_dynamics': 'bfgs',
    #"press_conv_thr" :'1.0d',
    # ! cell_dofree    ='volume',!'2Dxy', shape
    #"cell_dofree" :   'shape', #'z', #'volume', #!'2Dxy', 
                        # shape --shape keeps vol fixed and changes 
                        # lattce param ; 'z'--> only the z component
                        #  of axis 3 (v3_z) is moved
    },

#  'K_POINTS': {
#     'k-grid': [1, 1, 8,  # k-grid 
#                0, 0, 0,], # shift
#     # 'k-grid': 'gamma',
#     }

 }

posfiles=glob.glob(poscar_files) 
for ifile in posfiles:
    qe_parameters["&CONTROL"]['outdir'] += "_"+str(ifile) 
    qe_parameters["&CONTROL"]['prefix'] += '_'+str(ifile) 
    gen_qeinput.get_qe_input2(ifile, ps_info, qe_parameters, 
                              kwargs=None, lprint_cell ='angstrom', 
                              cal_type=cal_type, lcopy_pseudo=True)
  • Generate displacements from atomic positions in the poscar for vibrational calculations.

Example

import numpy as np
import esta
import esta.phonon.atm_displacements_selective_general_disp  as atmdisp

print('generating postion* files for displacement of selected atoms')
qe_part_file='qe_part'    #<-------not need to get poscar file s........MAKE It better ....TODO
posfile='fix_3_init_bi_POSCAR' #fix_rlx_3_4c_1_1e_POSCARPOSCAR'
delta_x = 0.02 # ang
atmdisp.gen_disp(posfile, qe_part_file, delta_x)
  • Get the electronic band gap from qe xml file

Example

import numpy as np
import glob
from esta import cf
import esta.qeBag.band_gap_xml as band_gap

xmls=glob.glob("*.xml")
for xmlfile in xmls: 
    egap, vbmdict, cbmdict = band_gap.eband_gap(xmlfile)
    #print ("bandgap : {} eV".format(egap))
    ##print ("bandgap : {} eV".format(egap*cf.har2ev))
    #print("vbM dict: {} ".format(vbmdict))
    #print("cbm dict: {} ".format(cbmdict))
  • Create ORCA input files for atomic relaxation from many xyz files: opt calculations

Example

  import glob
  import esta.orcaBag.input_orca as iorca
  import numpy as np

  cal_type = 'OPT' 

  nproc='10'
  memory='1000'

  #-----functional and basis(may contain additional tags) together-----------
  functional = "BP86"
  basis = " def2-SVP def2/J RIJCOSX "


  #-----None, True, or exact words-------------------------------------------
  dispersion='D3Zero' #True or None  # always needed!!

  #-----None or some solvent-------------------------------------------------
  solvent=None

  #-----None or some txt-----------------------------------------------------
  #extra_tags = {'tag1': 'int=ultrafine','tag2':'nosymm'}
  extra_tags = {'tag3':'NoUseSym '}

  #---charge and spin multiplicuty=2S+1 ; for unparied e- => spin-multi = 2; 
  #  unpaired=1
  charge  = 2
  multiplicity = 2
  #--------------------------------------------------------------------------

  xyz_file_list = glob.glob("*.xyz")
  print('xyz files are:', format(xyz_file_list))

  for ii in xyz_file_list:
      print('--**--**'*10)
      orca_obj = iorca.GenerateInp(ii, charge, multiplicity, cal_type)
      orca_obj.write_inp(functional=functional,basis=basis,dispersion=dispersion,\
              nproc=nproc, memory=memory, solvent=None, extra_tags=extra_tags)