Distributed Computation (SPMD)

.github/workflows/doc.yml

@@ -52,3 +52,4 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_build/html
+          keep_files: true

LICENSE

@@ -0,0 +1,201 @@
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README.md

@@ -1,31 +1,30 @@
 # Jrystal
 A JAX-based Differentiable Density Functional Theory Framework for Materials
 
+<div style="flex: 1; text-align: left;">
+    <img src="docs/images/jrystal_logo.png" alt="feature-solid" width="120"/>
+  </div>
+
+[**Reference docs**](https://sail-sg.github.io/jrystal/)
+
 ## Core Features
 
 <img src="docs/_static/images/feature-AD.png" alt="feature-AD" width="64" align="left"/>
 
-**Differentiable:** Leveraging JAX's automatic differentiation for efficient gradient computation of quantum properties, enabling straightforward optimization workflows.
-
-<br clear="all"/>
+**Differentiable:** Leveraging JAX's automatic differentiation for efficient gradient computation of quantum properties, enabling straightforward optimization workflows.  <br><br>
 
 <img src="docs/_static/images/feature-gpu.png" alt="feature-gpu" width="64" align="left"/>
 
-**GPU-Accelerated:** Optimized for modern GPU architectures, delivering high-performance quantum calculations with automatic hardware acceleration.
-
-<br clear="all"/>
+**GPU-Accelerated:** Optimized for modern GPU architectures, delivering high-performance quantum calculations with automatic hardware acceleration. <br><br>
 
 <img src="docs/_static/images/feature-solid.png" alt="feature-solid" width="64" align="left"/>
 
-**Solid-State Calculation:** Full-featured framework for periodic systems using plane wave basis sets, supporting precise electronic structure calculations of crystalline materials.
-
-<br clear="all"/>
+**Solid-State Calculation:** Full-featured framework for periodic systems using plane wave basis sets, supporting precise electronic structure calculations of crystalline materials. <br><br>
 
 <img src="docs/_static/images/feature-total.png" alt="feature-total" width="64" align="left"/>
 
-**Direct Optimization:** A direct minimization approach that avoids SCF iterations, enabling smooth convergence and natural integration of machine learning methods, and advanced quantum chemistry methods into density functional theory calculations.
+**Direct Optimization:** A direct minimization approach that avoids SCF iterations, enabling smooth convergence and natural integration of machine learning methods, and advanced quantum chemistry methods into density functional theory calculations. <br><br>
 
-<br clear="all"/>
 
 ## Installation
 
@@ -147,7 +146,3 @@ If you find this project useful, please cite:
 ## License
 
 This project is licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).
-
-## Documentation
-
-For detailed documentation, tutorials, and API reference, please visit our [documentation page](https://jrystal.readthedocs.io/).

config.yaml

@@ -5,20 +5,26 @@
 # Code will load the "$CRYSTAL.xyz" file in the geometry directory if
 # crystal name is provided, otherwise the code will read the from the path
 # specified by "crystal_file_path_path".
-crystal: "si"
+crystal: "diamond"
 crystal_file_path_path: null
+spin: 0  # number of unpaired electrons
 
+# The directory to save the results. If None, the code will not save the results under the current directory.
+save_dir: null
 ################################################
 #         Exchange-Correlation Setting         #
 ################################################
 # xc functional
-xc: "lda_x"
+# xc: "lda_x+lda_c_pw"
+xc: "gga_x_pbe+gga_c_pbe"
+# xc: "pbe"
 
 ################################################
 #           Pseudopotential Setting            #
 ################################################
 
-use_pseudopotential: False
+# if false, the code will use the all-electron calculation
+use_pseudopotential: true
 pseudopotential_file_dir: null
 # The pseudopotential file directory. If None, the code will use the default
 # pseudopotential file directory.
@@ -35,23 +41,23 @@ freq_mask_method: "spherical"
 # cutoff energy in Hartree
 cutoff_energy: 40
 # grid sizes for the FFT grid
-grid_sizes: 48
+grid_sizes: 32
 # k grid sizes for the Brillouin zone sampling using Monkhorst-Pack scheme
-k_grid_sizes: 1
+k_grid_sizes: [2, 2, 2]
 # Occupation method
-occupation: "gamma"
-# occupation support {"fermi-dirac", "gamma", "uniform"}
+occupation: "simplex-projector"
+# occupation support {"gamma", "uniform", "simplex-projector", "idempotent"}
 
 # smearing factor for the Fermi-Dirac distribution
-smearing: 0.0001
+smearing: 0.001
 # the total number of unoccupapied bands. The Total number of
 # potentially-occupied bands is ceil(num_electron / 2) + empty_bands
-empty_bands: 8
-spin_restricted: True
+empty_bands: 10
+spin_restricted: true
 # whether the calculation is spin_restricted or not, ie., spin-up and spin-down
 # electrons share the same spatial orbitals.
 
-# Hyperparameters for the Ewald sum.
+# Hyperparameters for the Ewald sum. nm,m
 ewald_args:
   ewald_eta: 0.1
   ewald_cutoff: 2.0e+4
@@ -63,6 +69,9 @@ epoch: 10000
 optimizer: "adam"
 optimizer_args:
   learning_rate: 0.01
+  b1: 0.9
+  b2: 0.99
+  # nesterov: false
 
 # arguments for the optimizer. Please refer to optax documentation.
 # https://optax.readthedocs.io/en/latest/api/optimizers.html
@@ -74,11 +83,12 @@ optimizer_args:
 scheduler: null
 # optax scheduler. No scheduler is used if set to None.
 
-convergence_condition: 1.e-8
+convergence_window_size: 20
+convergence_condition: 1.e-6
 # Convergence criterion for optimization.
-# The code monitors the variance of the objective values (e.g., energy)
-# over the last 50 steps (if available). If the computed variance meets
-# the convergence condition, the calculation will terminate.
+# The code monitors the standard deviation of the objective values (e.g.,energy)
+# over the last 50 steps (if available). If the computed standard deviation
+# meets the convergence condition, the calculation will terminate.
 
 ################################################
 # Band Structure Calculation Hyper-parameters. #
@@ -92,16 +102,15 @@ k_path_special_points: null
 # special points for the given unit cell, as defined in ASE.
 # For more details, refer to:
 # https://wiki.fysik.dtu.dk/ase/ase/dft/kpoints.html
-
-"k_path_special_points": "LGXL"
-num_kpoints: 60
+k_path_special_points: "LGXL"
+num_kpoints: 64
 
 # Alternatively, the user can provide a `k_path` file containing k-path
 # vectors. The file must be in `.npy` format and contain a 2D array,
 # where each row represents the relative coordinates of a k-point in
 # reciprocal space.
 k_path_file: null
-band_structure_epoch: 10000
+band_structure_epoch: 5000
 
 # Flag indicating whether fine-tuning is enabled.
 # If True, the optimization will start with the first k-point,
@@ -117,8 +126,16 @@ k_path_fine_tuning_epoch: 300
 # Random seed
 seed: 123
 
-# Environment setting
+# Jax Environment setting
 xla_preallocate: True
+# whether to use 64-bit precision for JAX operations
 jax_enable_x64: True
+
+# Enable the jax_debug_nans flag to automatically detect when NaNs are produced in jax.jit-compiled code
+jax_debug_nans: False
+
+# whether to print verbose output
 verbose: True
+
+# machine epsilon
 eps: 1.e-08

docs/_static/graph.js

@@ -1,6 +1,6 @@
 document.addEventListener("DOMContentLoaded", function() {
 
-  fetch("/_static/graph.dot?" + new Date().getTime())
+  fetch("_static/graph.dot?" + new Date().getTime())
     .then(function(response) {
       if (!response.ok) {
         throw new Error("Network response was not ok: " + response.statusText);