Z2pack with elk

CHANGE.log

@@ -4,3 +4,4 @@
 - Added fp.kpoint.wannier90_nnkpts and fp.kpoint.wannier90_full
 - In fp.System's input_files, and file_names, it is now required that the input is a list of strings (previously, a single string was also allowed).
 - Default saving is now JSON (change due to fsc.iohelper). Quiet loading doesn't ignore when the file ending is absent or serializer is not set.
+- Elk first principles (http://elk.sourceforge.net/) example files are included, and an additional function in kpoints.py was added to allow Z2pack to interface with Elk

examples/fp/elk/Bi/input/elk.in

@@ -0,0 +1,68 @@
+tasks
+0
+
+highq
+.true.
+
+spinorb
+.true.
+
+epsband
+1.e-8
+
+primcell
+.false.
+
+nempty
+10
+
+autoswidth
+.true.
+
+lmirep
+.true.
+
+sppath
+'/home-2/[email protected]/Z2pack/elk-6.8.4/species/'
+
+ngridk
+6 6 6
+
+
+
+! Atomic positions generated by spacegroup version 1.2.01
+!  Hermann-Mauguin symbol : R-3m:H
+!  Hall symbol            : -R 3 2"
+!  Schoenflies symbol     : D3d^5
+!  space group number     : 166:H
+!  lattice constants (a,b,c) :    8.590712580       8.590712580       22.41597726    
+!  angles in degrees (bc,ac,ab) :    90.00000000       90.00000000       120.0000000    
+!  number of conventional unit cells :    1   1   1
+!  reduction to primitive cell : T
+!  Wyckoff positions :
+!   species :    1, Bi
+!      0.000000000       0.000000000      0.2338900000    
+
+scale
+ 1.0
+
+scale1
+ 1.0
+
+scale2
+ 1.0
+
+scale3
+ 1.0
+
+avec
+   4.295356290       7.439775331       0.000000000    
+   8.590712580       0.000000000       0.000000000    
+  0.8881784197E-15   4.959850221      -7.471992420    
+
+atoms
+   1                                    : nspecies
+'Bi.in'                                 : spfname
+   2                                    : natoms; atpos, bfcmt below
+    0.46778000    0.26611000    0.29833000    0.00000000  0.00000000  0.00000000
+   -0.46778000   -0.26611000   -0.29833000    0.00000000  0.00000000  0.00000000

examples/fp/elk/Bi/input/elkWannBands.in

@@ -0,0 +1,86 @@
+tasks
+1
+550
+
+reducek
+0
+
+highq
+.true.
+
+spinorb
+.true.
+
+epsband
+1.e-8
+
+primcell
+.false.
+
+nempty
+10
+
+autoswidth
+.true.
+
+lmirep
+.true.
+
+sppath
+'/home-2/[email protected]/Z2pack/elk-6.8.4/species/'
+
+
+idxw90
+1-29
+
+num_iter
+0
+
+maxscl
+1
+
+! Atomic positions generated by spacegroup version 1.2.01
+!  Hermann-Mauguin symbol : R-3m:H
+!  Hall symbol            : -R 3 2"
+!  Schoenflies symbol     : D3d^5
+!  space group number     : 166:H
+!  lattice constants (a,b,c) :    8.590712580       8.590712580       22.41597726
+!  angles in degrees (bc,ac,ab) :    90.00000000       90.00000000       120.0000000
+!  number of conventional unit cells :    1   1   1
+!  reduction to primitive cell : T
+!  Wyckoff positions :
+!   species :    1, Bi
+!      0.000000000       0.000000000      0.2338900000
+
+scale
+ 1.0
+
+scale1
+ 1.0
+
+scale2
+ 1.0
+
+scale3
+ 1.0
+
+avec
+   4.295356290       7.439775331       0.000000000
+   8.590712580       0.000000000       0.000000000
+  0.8881784197E-15   4.959850221      -7.471992420
+
+atoms
+   1                                    : nspecies
+'Bi.in'                                 : spfname
+   2                                    : natoms; atpos, bfcmt below
+    0.46778000    0.26611000    0.29833000    0.00000000  0.00000000  0.00000000
+   -0.46778000   -0.26611000   -0.29833000    0.00000000  0.00000000  0.00000000
+
+
+
+xlwin
+postproc_setup : true
+begin projections
+random
+end projections
+shell_list 1

examples/fp/elk/Bi/run.py

@@ -0,0 +1,75 @@
+# -*- coding: utf-8 -*-
+'''
+run.py can be used to interface ELK and Z2Pack. To use, change elkdir to your location of elk.
+Wannier90 is run by Elk in library mode. Check http://elk.sourceforge.net/ for installation
+instructions.
+'''
+import os
+import shutil
+import subprocess
+
+import matplotlib.pyplot as plt
+import z2pack
+
+# Edit the paths to your Elk and Wannier90 here
+elkdir = '$HOME/Z2pack/elk-6.8.4/src/elk'
+
+# creating the results folder, running the SCF calculation if needed
+if not os.path.exists('./plots'):
+    os.mkdir('./plots')
+if not os.path.exists('./results'):
+    os.mkdir('./results')
+if not os.path.exists('./ground'):
+    os.makedirs('./ground')
+    print("Running the ground state calculation")
+    #do initial ground-state calculation in the ground folder using elk.in in the input folder
+    shutil.copyfile('input/elk.in', 'ground/elk.in')
+    subprocess.call(elkdir + ' >& elkWannier.log', shell=True, cwd='./ground')
+
+# Collecting the files for the surface calculation
+# The k-point nearest neighbors list/kpoints string is appended to the .in file,
+# starting on the last line, and there can be no extra lines in between the shell_list
+# and the nnkpts lines. The nnkpts line should be added directly to the end of elkWannBands.in
+# automatically by Z2pack during the surface calculation (becomes build/elk.in).
+input_files = [
+    'ground/' + name for name in [
+        "elk.in", "STATE.OUT", "INFO.OUT", "GEOMETRY.OUT", "LINENGY.OUT",
+        "DTOTENERGY.OUT", "EFERMI.OUT", "EIGVAL.OUT", "EQATOMS.OUT",
+        "EVALCORE.OUT", "EVALFV.OUT", "EVALSV.OUT", "EVECFV.OUT", "EVECSV.OUT",
+        "FERMIDOS.OUT", "GAP.OUT", "GEOMETRY.OUT", "IADIST.OUT", "LATTICE.OUT",
+        "KPOINTS.OUT", "MOMENT.OUT", "MOMENTM.OUT", "OCCSV.OUT", "RMSDVS.OUT",
+        "SYMCRYS.OUT", "SYMLAT.OUT", "SYMSITE.OUT", "TOTENERGY.OUT"
+    ]
+]
+
+# Note that this ensures that elkWannBands.in is used
+# rather than what was used for the Ground state calculation.
+shutil.copyfile('input/elkWannBands.in', 'ground/elk.in')
+
+# Create the Z2Pack system.
+system = z2pack.fp.System(
+    input_files=input_files,
+    kpt_fct=z2pack.fp.kpoint.elk,
+    kpt_path="elk.in",
+    command=elkdir + ' >& elk.log',
+    mmn_path='wannier.mmn'
+)
+
+# Run the WCC calculations
+result_0 = z2pack.surface.run(
+    system=system,
+    surface=lambda s, t: [0, s / 2, t],
+    save_file='./results/res_0.json',
+    load=True
+)
+
+print(
+    'Z2 topological invariant at kx = 0: {0}'.format(
+        z2pack.invariant.z2(result_0)
+    )
+)
+
+# Plot the WCC
+fig, ax = plt.subplots(1, 1, sharey=True, figsize=(9, 5))
+z2pack.plot.wcc(result_0, axis=ax)
+plt.savefig('plots/plot.pdf', bbox_inches='tight')

examples/fp/elk/Bi2Se3/clean.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+rm -rf ground build results plots

examples/fp/elk/Bi2Se3/input/elk.in

@@ -0,0 +1,91 @@
+tasks
+0
+20
+
+highq
+.true.
+
+spinorb
+.true.
+
+epsband
+1.e-8
+
+primcell
+.false.
+
+nempty
+10
+
+autoswidth
+.true.
+
+lmirep
+.true.
+
+sppath
+'/home-2/[email protected]/Z2pack2/elk-6.8.4/species/'
+
+ngridk
+12 12 5
+
+idxw90
+1-112
+
+xlwin
+postproc_setup : true
+begin projections
+random
+end projections
+
+plot1d
+4 400
+0.677219 0.322781 0.500000 :B
+0.000000 0.000000 0.500000 :Z
+0.000000 0.000000 0.000000 :gamma
+0.67721904 0.33860952 0.33860952 :X
+
+! Atomic positions generated by spacegroup version 1.2.01
+!  Hermann-Mauguin symbol : R-3m:R
+!  Hall symbol            : -P 3* 2
+!  Schoenflies symbol     : D3d^5
+!  space group number     : 166:R
+!  lattice constants (a,b,c) :    18.59302275       18.59302275       18.59302275    
+!  angles in degrees (bc,ac,ab) :    24.40000000       24.40000000       24.40000000    
+!  number of conventional unit cells :    1   1   1
+!  reduction to primitive cell : T
+!  Wyckoff positions :
+!   species :    1, Bi
+!     0.3990000000      0.3990000000      0.3990000000    
+!   species :    2, Se
+!      0.000000000       0.000000000       0.000000000    
+!     0.7940000000      0.7940000000      0.7940000000    
+
+scale
+ 1.0
+
+scale1
+ 1.0
+
+scale2
+ 1.0
+
+scale3
+ 1.0
+
+avec
+   1.660660727      -3.660906252      -6.752286776    
+   1.660660727      -7.680860062       0.000000000    
+   18.59302275       0.000000000       0.000000000    
+
+atoms
+   2                                    : nspecies
+'Bi.in'                                 : spfname
+   2                                    : natoms; atpos, bfcmt below
+    0.10100000    0.10100000    0.19700000    0.00000000  0.00000000  0.00000000
+   -0.10100000   -0.10100000   -0.19700000    0.00000000  0.00000000  0.00000000
+'Se.in'                                 : spfname
+   3                                    : natoms; atpos, bfcmt below
+    0.50000000    0.50000000    0.00000000    0.00000000  0.00000000  0.00000000
+   -0.29400000   -0.29400000    0.38200000    0.00000000  0.00000000  0.00000000
+    0.29400000    0.29400000   -0.38200000    0.00000000  0.00000000  0.00000000