merge master into lmpotf

mir-group · Jun 7, 2024 · d4281e7 · d4281e7
2 parents 3457c30 + 700f2c8
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diff --git a/.github/workflows/flare.yml b/.github/workflows/flare.yml
@@ -16,7 +16,8 @@ jobs:
       matrix:
         omp: [OFF, ON]
         lapack: [OFF, ON]
-    name: "(OpenMP, Lapack) ="
+        python-version: ["3.7", "3.8"]
+    name: "(OpenMP, Lapack, Python) ="
 
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
@@ -30,35 +31,10 @@ jobs:
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - uses: actions/checkout@v2
-
-    - name: Install Sphinx and Breathe
-      run: |
-        sudo apt-get update
-        sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx
-
-    - name: Run Doxygen
-      uses: mattnotmitt/[email protected]
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
       with:
-        # Path to Doxyfile
-        doxyfile-path: "./Doxyfile" # default is ./Doxyfile
-        # Working directory
-        working-directory: "./docs" # default is .
-
-    - name: Run Sphinx
-      run: |
-        cd docs
-        pwd
-        ls
-        make html
-
-    - name: Publish the docs
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        # Default Doxyfile build documentation to html directory.
-        # Change the directory if changes in Doxyfile
-        publish_dir: ./docs/build/html
-      if: github.event_name == 'pull_request' && matrix.lapack == 'on' && matrix.omp == 'on'
+        python-version: ${{ matrix.python-version }}
 
     - name: Build
       run: |
@@ -82,27 +58,41 @@ jobs:
         echo "Lapack ${{ matrix.lapack }}"
 
         cmake ..
-        cmake --build . -j
+        cmake --build . -j4
         cp _C_flare* ../flare/bffs/sgp
         cd ctests
         ./tests
 
     - name: Install LAMMPS
       run: |
         git clone --depth 1 https://github.com/lammps/lammps.git lammps
+
+        cd lammps/src
+        cp pair_hybrid.* pair_lj_cut.* ..
+        rm pair_*.cpp pair_*.h
+        mv ../pair_hybrid.* ../pair_lj_cut.* .
+        cp MANYBODY/pair_tersoff.* .
+        rm MANYBODY/pair_*.*
+        rm MANYBODY/fix_*.*
+        mv pair_tersoff.* MANYBODY/
+        cp KOKKOS/pair_kokkos.* .
+        rm KOKKOS/pair_*.*
+        mv pair_kokkos.* KOKKOS/
+        cd ../..
+
         cd lammps_plugins
         ./install.sh $(pwd)/../lammps
         cd ..
         sudo cp -r ${BUILD_DIR}/External/Eigen3/Eigen /usr/include
         cd lammps
         mkdir build
         cd build
-        cmake ../cmake -DPKG_KOKKOS=ON -DKokkos_ENABLE_OPENMP=ON -DPKG_MANYBODY=yes
+        cmake ../cmake -DPKG_KOKKOS=ON -DKokkos_ENABLE_OPENMP=ON -DPKG_MANYBODY=ON
         make -j4
 
     - name: Pip install
       run: |
-        pip install -U codecov pytest pytest-cov pytest_mock
+        pip install -U codecov pytest pytest-cov pytest_mock Sphinx sphinx-rtd-theme breathe nbsphinx
         pip install -r requirements.txt
 
     - name: Patch ASE
@@ -122,6 +112,35 @@ jobs:
         cd tests
         pytest test_lammps.py
 
+    - name: Install Sphinx and Breathe
+      run: |
+        sudo apt-get update
+        sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx
+        
+    - name: Run Doxygen
+      uses: mattnotmitt/[email protected]
+      with:
+        # Path to Doxyfile
+        doxyfile-path: "./Doxyfile" # default is ./Doxyfile
+        # Working directory
+        working-directory: "./docs" # default is .
+
+    - name: Run Sphinx
+      run: |
+        cd docs
+        pwd
+        ls
+        make html
+        
+    - name: Publish the docs
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        # Default Doxyfile build documentation to html directory.
+        # Change the directory if changes in Doxyfile
+        publish_dir: ./docs/build/html
+      if: github.event_name == 'pull_request' && matrix.lapack == 'on' && matrix.omp == 'on'
+
 #     - name: Run tutorial
 #       run: |
 #         cd tests

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -112,6 +112,7 @@ set(FLARE_SOURCES
     src/flare_pp/descriptors/four_body.cpp
     src/flare_pp/kernels/kernel.cpp
     src/flare_pp/kernels/normalized_dot_product.cpp
+    src/flare_pp/kernels/dot_product.cpp
     src/flare_pp/kernels/norm_dot_icm.cpp
     src/flare_pp/kernels/squared_exponential.cpp)
 

diff --git a/README.md b/README.md
@@ -1,4 +1,6 @@
-[![Build Status](https://github.com/mir-group/flare/actions/workflows/main.yml/badge.svg)](https://github.com/mir-group/flare/actions) [![documentation](https://readthedocs.org/projects/flare/badge/?version=latest)](https://readthedocs.org/projects/flare) [![pypi](https://img.shields.io/pypi/v/mir-flare)](https://pypi.org/project/mir-flare/) [![activity](https://img.shields.io/github/commit-activity/m/mir-group/flare)](https://github.com/mir-group/flare/commits/master) [![codecov](https://codecov.io/gh/mir-group/flare/branch/master/graph/badge.svg)](https://codecov.io/gh/mir-group/flare)
+[![Build Status](https://github.com/mir-group/flare/actions/workflows/flare.yml/badge.svg)](https://github.com/mir-group/flare/actions) [![pypi](https://img.shields.io/pypi/v/mir-flare)](https://pypi.org/project/mir-flare/) [![activity](https://img.shields.io/github/commit-activity/m/mir-group/flare)](https://github.com/mir-group/flare/commits/master) [![codecov](https://codecov.io/gh/mir-group/flare/branch/master/graph/badge.svg)](https://codecov.io/gh/mir-group/flare)
+
+***NOTE: This is the latest release [1.3.3](https://github.com/mir-group/flare/releases/tag/1.3.3) which includes significant changes compared to the previous version [0.2.4](https://github.com/mir-group/flare/releases/tag/0.2.4). Please check the updated tutorials and documentations from the links below.***
 
 # FLARE: Fast Learning of Atomistic Rare Events
 
@@ -88,14 +90,22 @@ pytest
 ```
 
 ## References
-- If you use FLARE++ including B2 descriptors, NormalizedDotProduct kernel and Sparse GP, please cite the following paper:
+If you use FLARE++ including B2 descriptors, NormalizedDotProduct kernel and Sparse GP, please cite the following paper:
 
-  > [1] Vandermause, J., Xie, Y., Lim, J.S., Owen, C.J. and Kozinsky, B., 2021. *Active learning of reactive Bayesian force fields: Application to heterogeneous hydrogen-platinum catalysis dynamics.* [arXiv preprint arXiv:2106.01949](https://arxiv.org/abs/2106.01949).
+  > [1] Vandermause, J., Xie, Y., Lim, J.S., Owen, C.J. and Kozinsky, B., 2021. *Active learning of reactive Bayesian force fields: Application to heterogeneous hydrogen-platinum catalysis dynamics.* Nature Communications 13.1 (2022): 5183. https://www.nature.com/articles/s41467-022-32294-0
 
-- If you use FLARE active learning workflow, full Gaussian process or 2-body/3-body kernel in your research, please cite the following paper:
+If you use FLARE active learning workflow, full Gaussian process or 2-body/3-body kernel in your research, please cite the following paper:
 
   > [2] Vandermause, J., Torrisi, S. B., Batzner, S., Xie, Y., Sun, L., Kolpak, A. M. & Kozinsky, B. *On-the-fly active learning of interpretable Bayesian force fields for atomistic rare events.* npj Comput Mater 6, 20 (2020). https://doi.org/10.1038/s41524-020-0283-z
 
-- If you use FLARE LAMMPS pair style or MGP (mapped Gaussian process), please cite the following paper:
+If you use FLARE LAMMPS pair style or MGP (mapped Gaussian process), please cite the following paper:
 
   > [3] Xie, Y., Vandermause, J., Sun, L. et al. *Bayesian force fields from active learning for simulation of inter-dimensional transformation of stanene.* npj Comput Mater 7, 40 (2021). https://doi.org/10.1038/s41524-021-00510-y
+
+If you use FLARE PyLAMMPS for training, please cite the following paper:
+
+  > [4] Xie, Y., Vandermause, J., Ramakers, S., Protik, N.H., Johansson, A. and Kozinsky, B., 2022. *Uncertainty-aware molecular dynamics from Bayesian active learning: Phase Transformations and Thermal Transport in SiC.* npj Comput. Mater. 9(1), 36 (2023).
+
+If you use FLARE LAMMPS Kokkos pair style with GPU acceleration, please cite the following paper:
+
+  > [5] Johansson, A., Xie, Y., Owen, C.J., Soo, J., Sun, L., Vandermause, J. and Kozinsky, B., 2022. *Micron-scale heterogeneous catalysis with Bayesian force fields from first principles and active learning.* arXiv preprint arXiv:2204.12573.
diff --git a/ctests/test_kernels.cpp b/ctests/test_kernels.cpp
@@ -19,7 +19,7 @@ class KernelTest : public StructureTest {
 
 };
 
-using KernelTypes = ::testing::Types<SquaredExponential, NormalizedDotProduct>;
+using KernelTypes = ::testing::Types<SquaredExponential, NormalizedDotProduct, DotProduct>;
 TYPED_TEST_SUITE(KernelTest, KernelTypes);
 
 TYPED_TEST(KernelTest, TimeSelfKernel) {

diff --git a/ctests/test_sparse_gp.cpp b/ctests/test_sparse_gp.cpp
@@ -163,9 +163,11 @@ TEST_F(StructureTest, LikeGrad) {
   test_struc.forces = forces;
   test_struc.stresses = stresses;
 
-  sparse_gp.add_training_structure(test_struc);
+  sparse_gp.add_training_structure(test_struc, {-1}, 0.4, 0.2, 0.3);
   sparse_gp.add_all_environments(test_struc);
 
+  // TODO: add another test structure
+
   EXPECT_EQ(sparse_gp.Sigma.rows(), 0);
   EXPECT_EQ(sparse_gp.Kuu_inverse.rows(), 0);
 
@@ -194,8 +196,9 @@ TEST_F(StructureTest, LikeGrad) {
     like_down = sparse_gp.compute_likelihood_gradient(hyps_down);
 
     fin_diff = (like_up - like_down) / (2 * pert);
+    printf("like_grad=%lg, fin_diff=%lg\n", like_grad(i), fin_diff);
 
-    EXPECT_NEAR(like_grad(i), fin_diff, 1e-3 * abs(fin_diff));
+    EXPECT_NEAR(like_grad(i), fin_diff, 5e-3 * abs(fin_diff));
   }
 }
 
@@ -230,8 +233,19 @@ TEST_F(StructureTest, LikeGradStable) {
   test_struc.forces = forces;
   test_struc.stresses = stresses;
 
-  sparse_gp.add_training_structure(test_struc, {0, 1, 3, 5});
+  test_struc_2 = Structure(cell_2, species_2, positions_2, cutoff, dc);
+
+  Eigen::VectorXd energy_2 = Eigen::VectorXd::Random(1);
+  Eigen::VectorXd forces_2 = Eigen::VectorXd::Random(n_atoms * 3);
+  Eigen::VectorXd stresses_2 = Eigen::VectorXd::Random(6);
+  test_struc_2.energy = energy_2;
+  test_struc_2.forces = forces_2;
+  test_struc_2.stresses = stresses_2;
+
+  sparse_gp.add_training_structure(test_struc, {-1}, 0.4, 0.2, 0.3);
   sparse_gp.add_specific_environments(test_struc, {0, 1, 3}); 
+  sparse_gp.add_training_structure(test_struc_2, {0, 1, 3, 5}, 0.64, 0.55, 0.45);
+  sparse_gp.add_specific_environments(test_struc_2, {2, 3, 4}); 
 
   EXPECT_EQ(sparse_gp.Sigma.rows(), 0);
   EXPECT_EQ(sparse_gp.Kuu_inverse.rows(), 0);
@@ -282,8 +296,8 @@ TEST_F(StructureTest, LikeGradStable) {
     fin_diff = (like_up - like_down) / (2 * pert);
 
     std::cout << like_grad(i) << " " << fin_diff << std::endl;
-    EXPECT_NEAR(like_grad(i), fin_diff, 1e-5);
-    EXPECT_NEAR(like_grad(i), like_grad_original(i), 1e-6);
+    EXPECT_NEAR(like_grad(i), fin_diff, 1e-5 * abs(fin_diff));
+    EXPECT_NEAR(like_grad(i), like_grad_original(i), 1e-6 * abs(fin_diff));
   }
 }
 
@@ -320,14 +334,14 @@ TEST_F(StructureTest, Set_Hyps) {
 
   // Add sparse environments and training structures.
   std::cout << "adding training structure" << std::endl;
-  sparse_gp_1.add_training_structure(test_struc);
-  sparse_gp_1.add_training_structure(test_struc_2);
+  sparse_gp_1.add_training_structure(test_struc, {-1}, 0.1, 0.2, 0.3);
+  sparse_gp_1.add_training_structure(test_struc_2, {-1}, 0.5, 0.4, 0.6);
   sparse_gp_1.add_all_environments(test_struc);
   sparse_gp_1.add_all_environments(test_struc_2);
 
   std::cout << "adding training structure" << std::endl;
-  sparse_gp_2.add_training_structure(test_struc);
-  sparse_gp_2.add_training_structure(test_struc_2);
+  sparse_gp_2.add_training_structure(test_struc, {-1}, 0.1, 0.2, 0.3);
+  sparse_gp_2.add_training_structure(test_struc_2, {-1}, 0.5, 0.4, 0.6);
   sparse_gp_2.add_all_environments(test_struc);
   sparse_gp_2.add_all_environments(test_struc_2);
 

diff --git a/ctests/test_structure.h b/ctests/test_structure.h
@@ -5,6 +5,7 @@
 #include "structure.h"
 #include "four_body.h"
 #include "normalized_dot_product.h"
+#include "dot_product.h"
 #include "norm_dot_icm.h"
 #include "squared_exponential.h"
 #include "structure.h"

diff --git a/docs/source/citing.rst b/docs/source/citing.rst
@@ -3,7 +3,7 @@ How to Cite
 
 If you use FLARE++ including B2 descriptors, NormalizedDotProduct kernel and Sparse GP, please cite the following paper:
 
-  [1] Vandermause, J., Xie, Y., Lim, J.S., Owen, C.J. and Kozinsky, B., 2021. *Active learning of reactive Bayesian force fields: Application to heterogeneous hydrogen-platinum catalysis dynamics.* [arXiv preprint arXiv:2106.01949](https://arxiv.org/abs/2106.01949).
+  [1] Vandermause, J., Xie, Y., Lim, J.S., Owen, C.J. and Kozinsky, B., 2021. *Active learning of reactive Bayesian force fields: Application to heterogeneous hydrogen-platinum catalysis dynamics.* Nature Communications 13.1 (2022): 5183. https://www.nature.com/articles/s41467-022-32294-0
 
 If you use FLARE active learning workflow, full Gaussian process or 2-body/3-body kernel in your research, please cite the following paper:
 
@@ -13,4 +13,12 @@ If you use FLARE LAMMPS pair style or MGP (mapped Gaussian process), please cite
 
   [3] Xie, Y., Vandermause, J., Sun, L. et al. *Bayesian force fields from active learning for simulation of inter-dimensional transformation of stanene.* npj Comput Mater 7, 40 (2021). https://doi.org/10.1038/s41524-021-00510-y
 
+If you use FLARE PyLAMMPS for training, please cite the following paper:
+
+  [4] Xie, Y., Vandermause, J., Ramakers, S., Protik, N.H., Johansson, A. and Kozinsky, B., 2022. *Uncertainty-aware molecular dynamics from Bayesian active learning: Phase Transformations and Thermal Transport in SiC.* npj Comput. Mater. 9(1), 36 (2023).
+
+If you use FLARE LAMMPS Kokkos pair style with GPU acceleration, please cite the following paper:
+
+  [5] Johansson, A., Xie, Y., Owen, C.J., Soo, J., Sun, L., Vandermause, J. and Kozinsky, B., 2022. *Micron-scale heterogeneous catalysis with Bayesian force fields from first principles and active learning.* arXiv preprint arXiv:2204.12573.
+
 Thank you for using FLARE!
diff --git a/docs/source/installation/install.rst b/docs/source/installation/install.rst
@@ -14,24 +14,24 @@ Requirements
 
 2. Use conda to install compilers and dependencies for flare
 
-* Option 1: If you want to install flare with mkl
+* Option 1: You can load modules if your machine have already installed them (with mkl)
+
+.. code-block:: bash
+
+    module load cmake/3.17.3 gcc/9.3.0 intel-mkl/2017.2.174
+
+* Option 2: If you want to install flare with mkl
 
 .. code-block:: bash
 
     conda install -y gcc gxx cmake mkl-devel mkl-service mkl_fft openmp -c conda-forge
     
-* Option 2: If you want to install flare with openblas + lapacke
+* Option 3: If you want to install flare with openblas + lapacke
 
 .. code-block:: bash
 
     conda install -y gcc gxx cmake openmp liblapacke openblas -c conda-forge
 
-* Option 3: You can load modules if your machine have already installed them
-
-.. code-block:: bash
-
-    module load cmake/3.17.3 gcc/9.3.0 intel-mkl/2017.2.174
-
 3. Download flare code from github repo and pip install 
 
 .. code-block:: bash
@@ -107,6 +107,13 @@ Trouble shooting
 
     * the `ldd` command above should show the linked libraries in the `.conda/envs/flare` directory
 
+* If you encounter `Intel MKL FATAL ERROR` when running flare (after the compilation has done), this is likely a static library linkage issue. You can set up the environmental variable
+
+.. code-block:: bash
+
+    export LD_PRELOAD=${CONDA_PREFIX}/lib/libmkl_core.so:${CONDA_PREFIX}/lib/libmkl_intel_thread.so:${CONDA_PREFIX}/lib/libiomp5.so
+
+as instructed in `this discussion <https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/mkl-fails-to-load/m-p/1155538>`_.
 
 *****************************************
 Acceleration with multiprocessing and MKL