Develop (#250)

* 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 <[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 (#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 <[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 * 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 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]> Co-authored-by: Janosh Riebesell <[email protected]>
usnistgov · Aug 28, 2022 · 10219ea · 10219ea
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diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -54,7 +54,7 @@ Keras-Preprocessing==1.1.2
 kiwisolver==1.3.2
 libclang==12.0.0
 lightgbm==3.3.1
-lxml==4.7.1
+lxml==4.9.1
 Markdown==3.3.6
 MarkupSafe==2.0.1
 matplotlib==3.5.1
@@ -63,7 +63,7 @@ mpmath==1.2.1
 multitasking==0.0.10
 networkx==2.6.3
 ntlm-auth==1.5.0
-numpy==1.20.0
+numpy==1.22.0
 oauthlib==3.1.1
 opencv-python==4.5.4.60
 opt-einsum==3.3.0
@@ -128,8 +128,8 @@ sympy==1.9
 tensorboard
 tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
-tensorflow==2.8.0
-tensorflow-estimator==2.7.0
+tensorflow==2.8.1
+tensorflow-estimator==2.8
 tensorflow-io-gcs-filesystem==0.23.1
 termcolor==1.1.0
 threadpoolctl==3.0.0
@@ -148,4 +148,4 @@ Werkzeug==2.0.2
 wrapt==1.13.3
 xmltodict==0.12.0
 yfinance==0.1.67
-zipp==3.6.0
+zipp==3.6.0
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -55,7 +55,7 @@ Keras-Preprocessing==1.1.2
 kiwisolver==1.3.2
 libclang==12.0.0
 lightgbm==3.3.1
-lxml==4.7.1
+lxml==4.9.1
 Markdown==3.3.6
 MarkupSafe==2.0.1
 matplotlib==3.5.1
@@ -64,7 +64,7 @@ mpmath==1.2.1
 multitasking==0.0.10
 networkx==2.6.3
 ntlm-auth==1.5.0
-numpy==1.20.0
+numpy==1.22.0
 oauthlib==3.1.1
 opencv-python==4.5.4.60
 opt-einsum==3.3.0
@@ -130,8 +130,8 @@ sympy==1.9
 tensorboard
 tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
-tensorflow==2.7.1
-tensorflow-estimator==2.7.0
+tensorflow==2.8.1
+tensorflow-estimator==2.8
 tensorflow-io-gcs-filesystem==0.23.1
 termcolor==1.1.0
 threadpoolctl==3.0.0
@@ -150,4 +150,4 @@ Werkzeug==2.0.2
 wrapt==1.13.3
 xmltodict==0.12.0
 yfinance==0.1.67
-zipp==3.6.0
+zipp==3.6.0
diff --git a/docs/source/publications.rst b/docs/source/publications.rst
@@ -62,7 +62,6 @@ JARVIS-ML related
 
 [25. Recent advances and applications of deep learning methods in materials science, npj Computational Materials 8, 1 (2022)](https://www.nature.com/articles/s41524-022-00734-6)
 
-
 [26. Graph neural network predictions of metal organic framework CO2 adsorption properties, Comp. Mat. Sci., 210, 111388 (2022)](https://www.sciencedirect.com/science/article/pii/S092702562200163X)
 
 [27. Data-Driven Multi-Scale Modeling and Optimization for Elastic Properties of Cubic Microstructures](https://link.springer.com/article/10.1007/s40192-022-00258-3)
@@ -75,11 +74,13 @@ JARVIS-ML related
 
 [31. Designing High-Tc Superconductors with BCS-inspired Screening, Density Functional Theory and Deep-learning](https://arxiv.org/abs/2205.00060)
 
+[32. Rapid Prediction of Phonon Structure and Properties using an Atomistic Line Graph Neural Network (ALIGNN)](https://arxiv.org/abs/2207.12510)
+
 JARVIS-QC related
 -----------------------------------------------------
-[32. Quantum Computation for Predicting Electron and Phonon Properties of Solids., J. Phys.: Cond. Matt.](https://iopscience.iop.org/article/10.1088/1361-648X/ac1154)
+[33. Quantum Computation for Predicting Electron and Phonon Properties of Solids., J. Phys.: Cond. Matt.](https://iopscience.iop.org/article/10.1088/1361-648X/ac1154)
 
 
 JARVIS-QETB related
 -----------------------------------------------------
-[33. Quantum Computation for Predicting Electron and Phonon Properties of Solids., J. Phys.: Cond. Matt.](https://iopscience.iop.org/article/10.1088/1361-648X/ac1154)
+[34. Fast and Accurate Prediction of Material Properties with Three-Body Tight-Binding Model for the Periodic Table](https://arxiv.org/abs/2112.11585)
diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,5 +1,5 @@
 """Version number."""
-__version__ = "2022.07.17"
+__version__ = "2022.08.27"
 
 import os
 

diff --git a/jarvis/analysis/phonon/dos.py b/jarvis/analysis/phonon/dos.py
@@ -0,0 +1,62 @@
+"""Module to analyze phonon dos."""
+
+import numpy as np
+
+icm_to_eV = 1.23981e-4
+hbar = 6.582119569e-16  # eV*s
+kB = 8.617333262145e-5  # eV/K
+e = 1.60217662e-19
+Na = 6.0221409e23
+
+
+class PhononDos(object):
+    """Module to analyze phonon dos."""
+
+    def __init__(self, phonon_dos=[], phonon_freq_cm=[]):
+        """Initialize class."""
+        self.phonon_dos = phonon_dos
+        self.phonon_freq_cm = phonon_freq_cm
+
+    def debye_temperature(self, atoms=None):
+        """Get Debye temperature."""
+        # http://dx.doi.org/10.1103/PhysRevB.89.024304
+        # Eq. 10
+        n = atoms.num_atoms
+        omega = np.array(self.phonon_freq_cm) * icm_to_eV
+        gomega = np.array(self.phonon_dos)
+        integ = np.trapz(omega ** 2 * gomega, omega) / np.trapz(gomega, omega)
+        prefact = 1 / kB
+        # TODO: check if np.pi / 2 is required
+        moment_debye = (
+            n ** (-1 / 3)
+            * (prefact)
+            * np.sqrt(5 / 3 * integ)
+            # np.pi / 2 * n ** (-1 / 3) * (prefact) * np.sqrt(5 / 3 * integ)
+        )
+        return moment_debye
+
+    def heat_capacity(self, temperature=300):
+        """Get heat capacity at a temperature."""
+        omega = np.array(self.phonon_freq_cm) * icm_to_eV
+        # http://www.columbia.edu/~jh2228/phonons_thermal_hone.pdf
+        # Eq. 1
+        dos = np.array(self.phonon_dos) / icm_to_eV
+        x = (omega) / (kB * temperature)
+        Cp = (
+            kB
+            * x[1:] ** 2
+            * (np.exp(x[1:]) / (np.exp(x[1:]) - 1) ** 2)
+            * dos[1:]
+        )
+        Cp = np.insert(Cp, 0, 0)
+        return np.trapz(Cp, omega) * e * Na
+
+    def vibrational_entropy(self, temperature=300):
+        """Get heat vibrational entropy at a temperature."""
+        omega = np.array(self.phonon_freq_cm) * icm_to_eV
+        dos = np.array(self.phonon_dos) / icm_to_eV
+        x = (omega) / (kB * temperature)
+        n = 1 / (np.exp(x[1:]) - 1)
+        S_vib = kB * ((n + 1) * np.log(n + 1) + n * np.log(n)) * dos[1:]
+        S_vib = np.insert(S_vib, 0, S_vib[0])
+        return S_vib