Develop (usnistgov#216)

* Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (usnistgov#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (usnistgov#197) * Develop (usnistgov#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (usnistgov#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. * Add installation tests (usnistgov#214) * QE inputs, XANES, GHAction updates. (usnistgov#210) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (usnistgov#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (usnistgov#197) * Develop (usnistgov#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (usnistgov#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Add installation tests * Fix codestyle * Fix codestyle with black * Add docstrings * Fix pydocstyle error * Update __init__.py * Update __init__.py Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Adding QE super. * Minor changes to QE module, atoms xyz fix. * Adding qe_tb info, and version update. * Update __init__.py Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> Co-authored-by: Saurav Maheshkar <[email protected]>
RamyaGuru · Jan 13, 2022 · b48e113 · b48e113
1 parent 02f9794
commit b48e113
Show file tree

Hide file tree

Showing 12 changed files with 423 additions and 69 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -16,4 +16,6 @@ omit =
     */job*.py
     */restapi*.py
     */_xml*.py
+    */qe.py
+    */super.py
     tequila/*.py
diff --git a/docs/source/databases.rst b/docs/source/databases.rst
@@ -10,6 +10,7 @@ Database name            Number of data-points       Description
                                                      computed with OptB88vdW and TBmBJ methods             
 ``dft_2d``               1079                        Various 2D materials properties in JARVIS-DFT database  
                                                      computed with OptB88vdW                                
+``qe_tb``                829574                      Various 3D materials properties in JARVIS-QETB database  
 ``stm``                  1132                        2D materials STM images in JARVIS-STM database  
 ``wtbh_electron``        1440                        3D and 2D materials Wannier tight-binding Hamiltonian
                                                      dtaabase for electrons with spin-orbit coupling

diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,2 +1,12 @@
 """Version number."""
-__version__ = "2021.12.16"
+__version__ = "2022.01.10"
+
+import os
+
+
+def test(*args):
+    """Run pytest in the base of jarvis."""
+    import pytest
+
+    path = os.path.join(os.path.split(__file__)[0], "tests")
+    pytest.main(args=[path] + list(args))
diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py
@@ -14,6 +14,7 @@
 import os
 import math
 import tempfile
+import random
 
 amu_gm = 1.66054e-24
 ang_cm = 1e-8
@@ -580,6 +581,12 @@ def from_xyz(self, filename="dsgdb9nsd_057387.xyz", box_size=40):
         f = open(filename, "r")
         lines = f.read().splitlines()
         f.close()
+        try:
+            lattice_mat = np.array(lines[1].split(","), dtype="float").reshape(
+                3, 3
+            )
+        except Exception:
+            pass
         coords = []
         species = []
         natoms = int(lines[0])
@@ -764,6 +771,7 @@ def get_all_neighbors(self, r=5, bond_tol=0.15):
         return np.array(neighbors, dtype="object")
 
     def get_neighbors_cutoffs(self, max_cut=10, r=5, bond_tol=0.15):
+        """Get neighbors within cutoff."""
         neighbors = self.get_all_neighbors(r=r, bond_tol=bond_tol)
         dists = np.hstack(([[xx[2] for xx in yy] for yy in neighbors]))
         hist, bins = np.histogram(dists, bins=np.arange(0.1, 10.2, 0.1))
@@ -815,6 +823,7 @@ def get_neighbors_cutoffs(self, max_cut=10, r=5, bond_tol=0.15):
     def atomwise_angle_and_radial_distribution(
         self, r=5, bond_tol=0.15, c_size=10, verbose=False
     ):
+        """Get atomwise distributions."""
         rcut1, rcut2, neighbors = self.get_neighbors_cutoffs(
             r=r, bond_tol=bond_tol
         )
@@ -1692,19 +1701,29 @@ def build_xanes_poscar(
     filename_with_prefix=False,
 ):
     """Generate POSCAR file for XANES, note the element ordering."""
-    from jarvis.core.utils import rand_select
+    # from jarvis.core.utils import rand_select
     from jarvis.analysis.structure.spacegroup import Spacegroup3D
 
     dims = get_supercell_dims(
         atoms, enforce_c_size=enforce_c_size, extend=extend
     )
+    # spg = Spacegroup3D(atoms)
+    # wyckoffs = spg._dataset["wyckoffs"]
+    # atoms.props = wyckoffs
     atoms = atoms.make_supercell_matrix(dims)
     spath = os.path.join(dir, "POSCAR-supercell.vasp")
     atoms.write_poscar(spath)
     spg = Spacegroup3D(atoms)
     wyckoffs = spg._dataset["wyckoffs"]
     atoms.props = wyckoffs
-    props = rand_select(atoms.props)
+    # print ('atoms.props',atoms.props)
+    el_props = []
+    elements = atoms.elements
+    for ii, i in enumerate(elements):
+        if i == selected_element:
+            el_props.append(ii)
+    choice = random.choice(el_props)
+    props = {atoms.props[choice]: choice}
     tmp_atoms = atoms
     for i, j in props.items():
         if tmp_atoms.elements[j] == selected_element:
@@ -1729,14 +1748,13 @@ def build_xanes_poscar(
             filename = os.path.join(dir, filename)
             added_strt.props = ["" for i in range(added_strt.num_atoms)]
             added_strt.write_poscar(filename)
-            f = open(filename, "r")
-            filedata = f.read()
-            f.close()
-
+            with open(filename, "r") as f:
+                filedata = f.read()
             newdata = filedata.replace("XANES", tmp_atoms.elements[j])
-            f = open(filename, "w")
-            f.write(newdata)
-            f.close()
+            with open(filename, "w") as f:
+                f.write(newdata)
+
+    return atoms
 
 
 # ['Mn ', 'Mn ', 'Ru ', 'U ']

diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py
@@ -152,7 +152,7 @@ def get_db_info():
             "https://ndownloader.figshare.com/files/29070555",
             "jqe_tb_folder.json",
             "Obtaining QETB dataset 860k...",
-            "https://www.nature.com/articles/s41524-020-00440-1",
+            "https://arxiv.org/abs/2112.11585",
         ],
         # https://doi.org/10.6084/m9.figshare.14812050
         "omdb": [

diff --git a/jarvis/io/qe/inputs.py b/jarvis/io/qe/inputs.py
@@ -102,10 +102,12 @@ def __init__(
             self.cell_params = input_params["cell"]
         else:
             self.cell_params = {}
-
         if "input" in input_params:
             self.input = input_params["input"]
-            if "amass(1)" not in input_params["input"]:
+            if (
+                "amass(1)" not in input_params["input"]
+                and "zasr" not in input_params["input"]
+            ):
                 for ii, jj in enumerate(self.atoms.uniq_species):
                     tmp = "amass(" + str(ii + 1) + ")"
                     input_params["input"][tmp] = str(

diff --git a/jarvis/io/qe/outputs.py b/jarvis/io/qe/outputs.py
@@ -44,7 +44,6 @@ def get_total_energy(self):
         energies = []
         for i in self.lines:
             if "total energy              =" in i:
-                print(i)
                 energy = float(i.split()[-2])
                 energies.append(energy)
         return float(energies[-1]) * ryd_to_ev
@@ -57,6 +56,15 @@ def get_efermi(self):
                 efs.append(float(i.split()[-2]))
         return efs[-1]
 
+    @property
+    def job_done(self):
+        """Check if job is completed."""
+        done = False
+        for i in self.lines:
+            if "JOB DONE." in i:
+                done = True
+        return done
+
     def get_band_enegies(self):
         """Get band energies in eV."""
         band_energies = []
@@ -381,9 +389,7 @@ class ProjHamXml(object):
 
     # Adapted from https://github.com/kfgarrity/TightlyBound.jl
     def __init__(
-        self,
-        filename="projham_K.xml",
-        data=None,
+        self, filename="projham_K.xml", data=None,
     ):
         """Initialize class."""
         self.filename = filename

diff --git a/jarvis/io/vasp/inputs.py b/jarvis/io/vasp/inputs.py
@@ -106,62 +106,65 @@ def to_string(self):
     def write_file(self, filename):
         """Write the Poscar object to a file."""
         # TODO: Use to_string instead of re-writing the code here
-        f = open(filename, "w")
-        header = (
-            str(self.comment)
-            + str("\n1.0\n")
-            + str(self.atoms.lattice_mat[0][0])
-            + " "
-            + str(self.atoms.lattice_mat[0][1])
-            + " "
-            + str(self.atoms.lattice_mat[0][2])
-            + "\n"
-            + str(self.atoms.lattice_mat[1][0])
-            + " "
-            + str(self.atoms.lattice_mat[1][1])
-            + " "
-            + str(self.atoms.lattice_mat[1][2])
-            + "\n"
-            + str(self.atoms.lattice_mat[2][0])
-            + " "
-            + str(self.atoms.lattice_mat[2][1])
-            + " "
-            + str(self.atoms.lattice_mat[2][2])
-            + "\n"
-        )
-        # order = np.argsort(self.atoms.elements)
-        coords = self.atoms.frac_coords
-        # DO NOT USE ORDER
-        coords_ordered = np.array(coords)  # [order]
-        elements_ordered = np.array(self.atoms.elements)  # [order]
-        props_ordered = np.array(self.atoms.props)  # [order]
-        # check_selective_dynamics = False
-        counts = get_counts(elements_ordered)
-        if "T" in "".join(map(str, self.atoms.props[0])):
-            middle = (
-                " ".join(map(str, counts.keys()))
+        with open(filename, "w") as f:
+            # f = open(filename, "w")
+            header = (
+                str(self.comment)
+                + str("\n1.0\n")
+                + str(self.atoms.lattice_mat[0][0])
+                + " "
+                + str(self.atoms.lattice_mat[0][1])
+                + " "
+                + str(self.atoms.lattice_mat[0][2])
                 + "\n"
-                + " ".join(map(str, counts.values()))
-                + "\nSelective dynamics\n"
-                + "Direct\n"
-            )
-        else:
-            middle = (
-                " ".join(map(str, counts.keys()))
+                + str(self.atoms.lattice_mat[1][0])
+                + " "
+                + str(self.atoms.lattice_mat[1][1])
+                + " "
+                + str(self.atoms.lattice_mat[1][2])
+                + "\n"
+                + str(self.atoms.lattice_mat[2][0])
+                + " "
+                + str(self.atoms.lattice_mat[2][1])
+                + " "
+                + str(self.atoms.lattice_mat[2][2])
                 + "\n"
-                + " ".join(map(str, counts.values()))
-                + "\ndirect\n"
             )
-        rest = ""
-        # print ('repr',self.frac_coords, self.frac_coords.shape)
-        for ii, i in enumerate(coords_ordered):
-            p_ordered = str(props_ordered[ii])
-            rest = rest + " ".join(map(str, i)) + " " + str(p_ordered) + "\n"
+            # order = np.argsort(self.atoms.elements)
+            coords = self.atoms.frac_coords
+            # DO NOT USE ORDER
+            coords_ordered = np.array(coords)  # [order]
+            elements_ordered = np.array(self.atoms.elements)  # [order]
+            props_ordered = np.array(self.atoms.props)  # [order]
+            # check_selective_dynamics = False
+            counts = get_counts(elements_ordered)
+            if "T" in "".join(map(str, self.atoms.props[0])):
+                middle = (
+                    " ".join(map(str, counts.keys()))
+                    + "\n"
+                    + " ".join(map(str, counts.values()))
+                    + "\nSelective dynamics\n"
+                    + "Direct\n"
+                )
+            else:
+                middle = (
+                    " ".join(map(str, counts.keys()))
+                    + "\n"
+                    + " ".join(map(str, counts.values()))
+                    + "\ndirect\n"
+                )
+            rest = ""
+            # print ('repr',self.frac_coords, self.frac_coords.shape)
+            for ii, i in enumerate(coords_ordered):
+                p_ordered = str(props_ordered[ii])
+                rest = (
+                    rest + " ".join(map(str, i)) + " " + str(p_ordered) + "\n"
+                )
 
-        result = header + middle + rest
+            result = header + middle + rest
 
-        f.write(result)
-        f.close()
+            f.write(result)
+            # f.close()
 
     @staticmethod
     def from_string(lines):

diff --git a/jarvis/tasks/qe/__init__.py b/jarvis/tasks/qe/__init__.py
@@ -0,0 +1 @@
+"""Module to run QE jobs."""