1#!/usr/local/bin/python3.8 2r""" 3Flow for e-Bands with frozen phonon 4=================================== 5 6Electronic band structure of silicon in a distorted geometry (frozen phonon at q=0) 7""" 8 9import sys 10import os 11import numpy as np 12import abipy.data as data 13import abipy.abilab as abilab 14import abipy.flowtk as flowtk 15 16 17def make_scf_nscf_inputs(structure, paral_kgb=1): 18 multi = abilab.MultiDataset(structure, pseudos=data.pseudos("14si.pspnc"), ndtset=2) 19 20 # Global variables 21 global_vars = dict( 22 ecut=6, 23 nband=8, 24 timopt=-1, 25 paral_kgb=0, 26 #nstep=4, # This is not enough to converge. Used to test the automatic restart. 27 nstep=10, 28 iomode=3, 29 ) 30 31 multi.set_vars(global_vars) 32 33 # Dataset 1 (GS run) 34 multi[0].set_kmesh(ngkpt=[8,8,8], shiftk=[0,0,0]) 35 multi[0].set_vars(tolvrs=1e-6) 36 37 # Dataset 2 (NSCF run) 38 kptbounds = [ 39 [0.5, 0.0, 0.0], # L point 40 [0.0, 0.0, 0.0], # Gamma point 41 [0.0, 0.5, 0.5], # X point 42 ] 43 44 multi[1].set_kpath(ndivsm=6, kptbounds=kptbounds) 45 multi[1].set_vars(tolwfr=1e-12) 46 47 # Generate two input files for the GS and the NSCF run 48 scf_input, nscf_input = multi.split_datasets() 49 50 return scf_input, nscf_input 51 52 53def build_flow(options): 54 # Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_") 55 if not options.workdir: 56 options.workdir = os.path.basename(sys.argv[0]).replace(".py", "").replace("run_", "flow_") 57 58 # build the structures 59 base_structure = abilab.Structure.from_file(data.cif_file("si.cif")) 60 modifier = abilab.StructureModifier(base_structure) 61 62 etas = [-0.1, 0, +0.1] 63 ph_displ = np.reshape(np.zeros(3*len(base_structure)), (-1,3)) 64 ph_displ[0,:] = [+1, 0, 0] 65 ph_displ[1,:] = [-1, 0, 0] 66 67 displaced_structures = modifier.displace(ph_displ, etas, frac_coords=False) 68 69 flow = flowtk.Flow(options.workdir, manager=options.manager) 70 71 for structure in displaced_structures: 72 # Create the work for the band structure calculation. 73 scf_input, nscf_input = make_scf_nscf_inputs(structure) 74 75 work = flowtk.BandStructureWork(scf_input, nscf_input) 76 flow.register_work(work) 77 78 return flow 79 80 81# This block generates the thumbnails in the AbiPy gallery. 82# You can safely REMOVE this part if you are using this script for production runs. 83if os.getenv("READTHEDOCS", False): 84 __name__ = None 85 import tempfile 86 options = flowtk.build_flow_main_parser().parse_args(["-w", tempfile.mkdtemp()]) 87 build_flow(options).graphviz_imshow() 88 89 90@flowtk.flow_main 91def main(options): 92 """ 93 This is our main function that will be invoked by the script. 94 flow_main is a decorator implementing the command line interface. 95 Command line args are stored in `options`. 96 """ 97 return build_flow(options) 98 99 100if __name__ == "__main__": 101 sys.exit(main()) 102 103 104############################################################################ 105# 106# Run the script with: 107# 108# run_phfrozen_ebands -s 109# 110# then use: 111# 112# abirun.py flow_phfrozen_ebands/ structures -v 113# 114# to analyze the input/output structures including the atomic positions: 115# 116# .. code-block:: bash 117# 118# Lattice parameters: 119# formula natom angle0 angle1 angle2 a b c volume \ 120# w0_t0_in Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 121# w0_t0_out Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 122# w0_t1_in Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 123# w1_t0_in Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 124# w1_t0_out Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 125# w1_t1_in Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 126# w2_t0_in Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 127# w2_t0_out Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 128# w2_t1_in Si2 2 60.0 60.0 60.0 3.867 3.867 3.867 40.888 129# 130# abispg_num P [GPa] Max|F| eV/ang task_class status 131# w0_t0_in None NaN NaN ScfTask Completed 132# w0_t0_out 12 -3.638 3.180e+00 ScfTask Completed 133# w0_t1_in None NaN NaN NscfTask Completed 134# w1_t0_in None NaN NaN ScfTask Completed 135# w1_t0_out 227 -5.212 7.430e-27 ScfTask Completed 136# w1_t1_in None NaN NaN NscfTask Completed 137# w2_t0_in None NaN NaN ScfTask Completed 138# w2_t0_out 12 -4.192 2.095e+00 ScfTask Completed 139# w2_t1_in None NaN NaN NscfTask Completed 140# 141# Atomic positions (columns give the site index): 142# 0 \ 143# w0_t0_in (Si, +0.970139 +0.000000 +0.014930) 144# w0_t0_out (Si, +0.970139 +0.000000 +0.014930) 145# w0_t1_in (Si, +0.970139 +0.000000 +0.014930) 146# w1_t0_in (Si, +0.000000 +0.000000 +0.000000) 147# w1_t0_out (Si, +0.000000 +0.000000 +0.000000) 148# w1_t1_in (Si, +0.000000 +0.000000 +0.000000) 149# w2_t0_in (Si, +0.029861 +0.000000 +0.985070) 150# w2_t0_out (Si, +0.029861 +0.000000 +0.985070) 151# w2_t1_in (Si, +0.029861 +0.000000 +0.985070) 152# 153# 1 status 154# w0_t0_in (Si, +0.279861 +0.250000 +0.235070) Completed 155# w0_t0_out (Si, +0.279861 +0.250000 +0.235070) Completed 156# w0_t1_in (Si, +0.279861 +0.250000 +0.235070) Completed 157# w1_t0_in (Si, +0.250000 +0.250000 +0.250000) Completed 158# w1_t0_out (Si, +0.250000 +0.250000 +0.250000) Completed 159# w1_t1_in (Si, +0.250000 +0.250000 +0.250000) Completed 160# w2_t0_in (Si, +0.220139 +0.250000 +0.264930) Completed 161# w2_t0_out (Si, +0.220139 +0.250000 +0.264930) Completed 162# w2_t1_in (Si, +0.220139 +0.250000 +0.264930) Completed 163# 164# Finally, we can plot the electronic bands with the command: 165# 166# abirun.py flow_phfrozen_ebands ebands -p -t NscfTask 167# 168# to select only the band structures produced by the NscfTask. 169# 170# .. image:: https://github.com/abinit/abipy_assets/blob/master/run_phfrozen_ebands.png?raw=true 171# :alt: Band structures of Si computed for different displacement amplitudes. 172# 173
