Develop (#270)

* 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 (#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. (#197) * Develop (#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 (#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 <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com> Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> * 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 (#214) * QE inputs, XANES, GHAction updates. (#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 (#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. (#197) * Develop (#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 (#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 <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com> Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> * 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 <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com> * 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 <writetokamal.1989@gmail.com> Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com> * Adding QE super. * Minor changes to QE module, atoms xyz fix. * Adding qe_tb info, and version update. * Update __init__.py * WIP super QE. * Working version of ScSi. * QE inputs and task update. * Add master super. * Add master super. * Lint fix. * Lint fix. * Minor fix. * ET update. * Fix ET test. * Update sanitize atoms. * Additonal checks on supercond. * Debye bug fix. * Pressure in QE Super. * Version fix, publication update, supercond workflow update. * Lint fix. * Tensorboard fix. * Tensorboard fix. * Tensorboard fix. * Melting temp fix. * Update vasp.py (#234) * Local tetra tmp. * Version update. * Lint fix. * HSE06 * Tmp. * Vacancy update, Optimade structureand other minor lint updates. * STEM pytest fix. * Minor lint fix. * Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms * Lint fix. * Added phononDos class. * fix pytorch UserWarning in build_undirected_edgedata() (#243) site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor. r = torch.tensor(r).type(torch.get_default_dtype()) * Add PhaseDiagram. * Add PhaseDiagram. * PhaseDiagram update. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * Compare atoms, get spg info directly from atoms. * Flake8 fix. * Update publications.rst * Update qiskit. * Update qiskit. * Update test_hermsolver.py * FIix qiskit DOS. * Update test_hermsolver.py * Fix linting. * Develop og (#257) * Added isotope scattering rate to phonon DOS analysis script. * Linting fix. * Linting fix. * Linting fix. * Add QE convergence. * Update converg.py. * Nexus. * Super with converg. * Super with converg. * SuperCon QE update. * Figshare DB update. * Figshare DB update. * Update alignn ff link. * Lint fix. * DB docs update. * Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy. * Lint fix. Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com> Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com> Co-authored-by: Ramya Gurunathan <ramya1006@gmail.com>
usnistgov · Jan 9, 2023 · bfac232 · bfac232
1 parent 29a9ddd
commit bfac232
Show file tree

Hide file tree

Showing 8 changed files with 38 additions and 31 deletions.
diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,5 +1,5 @@
 """Version number."""
-__version__ = "2022.12.11"
+__version__ = "2023.01.09"
 
 import os
 

diff --git a/jarvis/analysis/phonon/ir.py b/jarvis/analysis/phonon/ir.py
@@ -19,7 +19,7 @@ def normalize_vecs(phonon_eigenvectors, masses):
     nmasses = len(masses)
     natoms = nmasses
     sqrt_masses = np.sqrt(masses)
-    eigendisplacements = np.zeros((nmodes, natoms, 3), dtype=np.float64)
+    eigendisplacements = np.zeros((nmodes, natoms, 3), dtype="float64")
     for i in range(0, nmodes):
         eigenvector = phonon_eigenvectors[i]
         for j in range(0, natoms):

diff --git a/jarvis/core/lattice.py b/jarvis/core/lattice.py
@@ -54,7 +54,7 @@ def __init__(self, lattice_mat=None, round_off=5):
         >>> [round(i,2) for i in lat.lat_angles()]
         [90.0, 90.0, 90.0]
         """
-        tmp = np.array(lattice_mat, dtype=np.float64).reshape((3, 3))
+        tmp = np.array(lattice_mat, dtype="float64").reshape((3, 3))
         self._lat = np.around(tmp, decimals=round_off)
         self._inv_lat = None
         self._lll_matrix_mappings = {}
@@ -264,12 +264,12 @@ def get_points_in_sphere(self, frac_points, center, r):
         # Generate all possible images that could be within `r` of `center`
         mins = np.floor(pcoords - nmax)
         maxes = np.ceil(pcoords + nmax)
-        arange = np.arange(start=mins[0], stop=maxes[0], dtype=np.int)
-        brange = np.arange(start=mins[1], stop=maxes[1], dtype=np.int)
-        crange = np.arange(start=mins[2], stop=maxes[2], dtype=np.int)
-        arange = arange[:, None] * np.array([1, 0, 0], dtype=np.int)[None, :]
-        brange = brange[:, None] * np.array([0, 1, 0], dtype=np.int)[None, :]
-        crange = crange[:, None] * np.array([0, 0, 1], dtype=np.int)[None, :]
+        arange = np.arange(start=mins[0], stop=maxes[0], dtype="int")
+        brange = np.arange(start=mins[1], stop=maxes[1], dtype="int")
+        crange = np.arange(start=mins[2], stop=maxes[2], dtype="int")
+        arange = arange[:, None] * np.array([1, 0, 0], dtype="int")[None, :]
+        brange = brange[:, None] * np.array([0, 1, 0], dtype="int")[None, :]
+        crange = crange[:, None] * np.array([0, 0, 1], dtype="int")[None, :]
         tmp_cr = crange[None, None, :]
         images = arange[:, None, None] + brange[None, :, None] + tmp_cr
 
@@ -337,7 +337,7 @@ def get_angles(v1, v2, l1, l2):
             )
             for j, k in np.argwhere(inds):
                 scale_m = np.array(
-                    (f_a[i], f_b[j], f_c[k]), dtype=np.int
+                    (f_a[i], f_b[j], f_c[k]), dtype="int"
                 )  # type: ignore
                 if abs(np.linalg.det(scale_m)) < 1e-8:
                     continue
@@ -388,7 +388,7 @@ def _calculate_lll(self, delta=0.75):
 
         k = 2
 
-        mapping = np.identity(3, dtype=np.double)
+        mapping = np.identity(3, dtype="double")
         while k <= 3:
             # Size reduction.
             for i in range(k - 1, 0, -1):

diff --git a/jarvis/core/spectrum.py b/jarvis/core/spectrum.py
@@ -49,9 +49,9 @@ def smoothen_spiky_spectrum(self):
             self.min_x,
             self.max_x + self.resolution,
             self.resolution,
-            dtype=np.float64,
+            dtype="float",
         )
-        spect_y = np.zeros_like(spect_x, dtype=np.float64)
+        spect_y = np.zeros_like(spect_x, dtype="float")
         for i, j, k in zip(self.x, self.y, lwidth_list):
             spect_y += lorentzian(spect_x, j, i, k)
         return spect_x, spect_y

diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py
@@ -18,9 +18,9 @@
 from tqdm import tqdm
 import matplotlib.image as mpimg
 from jarvis.analysis.stm.tersoff_hamann import TersoffHamannSTM
-import matplotlib.pyplot as plt
 
-plt.switch_backend("agg")
+# import matplotlib.pyplot as plt
+# plt.switch_backend("agg")
 
 
 def get_db_info():
@@ -296,10 +296,15 @@ def get_stm_2d_dataset():
 def get_request_data(
     js_tag="jdft_2d-4-26-2020.json",
     url="https://ndownloader.figshare.com/files/22471019",
+    store_dir=None,
 ):
     """Get data with progress bar."""
     zfile = js_tag + ".zip"
-    path = str(os.path.join(os.path.dirname(__file__), zfile))
+    if store_dir is None:
+        path = str(os.path.join(os.path.dirname(__file__), zfile))
+    else:
+        path = str(os.path.join(store_dir, zfile))
+
     # path = str(os.path.join(os.path.dirname(__file__), js_tag))
     if not os.path.isfile(path):
         # zfile = str(os.path.join(os.path.dirname(__file__), "tmp.zip"))
@@ -329,7 +334,7 @@ def get_request_data(
     return data
 
 
-def data(dataset="dft_2d"):
+def data(dataset="dft_2d", store_dir=None):
     """Provide main function to download datasets."""
     db_info = get_db_info()
     if dataset not in list(db_info.keys()):
@@ -365,7 +370,7 @@ def data(dataset="dft_2d"):
     #        zipObj.extractall(os.path.join(os.path.dirname(__file__)))
     #    os.remove(zfile)
     # data = loadjson(path)
-    dat = get_request_data(js_tag=js_tag, url=url)
+    dat = get_request_data(js_tag=js_tag, url=url, store_dir=store_dir)
     return dat
 
 

diff --git a/jarvis/io/phonopy/fcmat2hr.py b/jarvis/io/phonopy/fcmat2hr.py
@@ -31,12 +31,16 @@ def get_phonon_hr(
     nrpt_max = 51 ** 3
     # hr matrix
     norbs = num_patom * 3
-    hr_mat = np.zeros((ndim, ndim, ndim, norbs, norbs), dtype=np.complex128)
-    hr_mat0 = np.zeros((nrpt_max, norbs, norbs), dtype=np.complex128)
+    hr_mat = np.zeros((ndim, ndim, ndim, norbs, norbs), dtype="complex128")
+    # hr_mat = np.zeros((ndim, ndim, ndim, norbs, norbs), dtype=np.complex128)
+    hr_mat0 = np.zeros((nrpt_max, norbs, norbs), dtype="complex128")
+    # hr_mat0 = np.zeros((nrpt_max, norbs, norbs), dtype=np.complex128)
     # WS points
-    rpts = np.zeros((nrpt_max, 3), dtype=np.int32)
+    rpts = np.zeros((nrpt_max, 3), dtype="int32")
+    # rpts = np.zeros((nrpt_max, 3), dtype=np.int32)
     # degeneracy
-    dege = np.zeros((nrpt_max), dtype=np.int32)
+    dege = np.zeros((nrpt_max), dtype="int32")
+    # dege = np.zeros((nrpt_max), dtype=np.int32)
 
     for iatom in range(num_patom):  # atoms in primitive cell
         for jatom in range(num_patom):  # atoms in primitive cell

diff --git a/jarvis/io/phonopy/inputs.py b/jarvis/io/phonopy/inputs.py
@@ -32,42 +32,40 @@ def prim_axis(self):
             if latt == "rhombohedral":
                 transf = (
                     np.array(
-                        [[2, -1, -1], [1, 1, -2], [1, 1, 1]], dtype=np.float
+                        [[2, -1, -1], [1, 1, -2], [1, 1, 1]], dtype="float"
                     )
                     / 3
                 )
             elif "I" in sgp:
                 transf = (
                     np.array(
-                        [[-1, 1, 1], [1, -1, 1], [1, 1, -1]], dtype=np.float
+                        [[-1, 1, 1], [1, -1, 1], [1, 1, -1]], dtype="float"
                     )
                     / 2
                 )
 
             elif "F" in sgp:
                 transf = (
-                    np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], dtype=np.float)
+                    np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], dtype="float")
                     / 2
                 )
             elif "A" in sgp:
                 transf = (
-                    np.array(
-                        [[2, 0, 0], [0, 1, -1], [0, 1, 1]], dtype=np.float
-                    )
+                    np.array([[2, 0, 0], [0, 1, -1], [0, 1, 1]], dtype="float")
                     / 2
                 )
             elif "C" in sgp:
                 if latt == "monoclinic":
                     transf = (
                         np.array(
-                            [[1, 1, 0], [-1, 1, 0], [0, 0, 2]], dtype=np.float
+                            [[1, 1, 0], [-1, 1, 0], [0, 0, 2]], dtype="float"
                         )
                         / 2
                     )
                 else:
                     transf = (
                         np.array(
-                            [[1, -1, 0], [1, 1, 0], [0, 0, 2]], dtype=np.float
+                            [[1, -1, 0], [1, 1, 0], [0, 0, 2]], dtype="float"
                         )
                         / 2
                     )

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2022.12.11",
+    version="2023.01.08",
     long_description=long_d,
     install_requires=[
         "numpy>=1.19.5",