Merge branch 'develop'

issp-center-dev · Nov 6, 2024 · 0a11803 · 0a11803
2 parents 7fa4b13 + abbb642
commit 0a11803
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diff --git a/.github/workflows/Test_abICS.yml b/.github/workflows/Test_abICS.yml
@@ -3,22 +3,25 @@
 
 name: Test for abICS
 
-on: [push]
+on:
+  push:
+  schedule:
+    - cron: '0 0 1,15 * *' # JST 9:00 on 1st and 15th every month
 
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-        testname: [Unit, Sampling, ActiveLearn]
+        python-version: ['3.9', '3.12']
+        testname: [Unit, Sampling, ActiveLearnAenet, ActiveLearnNequip, ActiveLearnMLIP-3]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -42,8 +45,14 @@ jobs:
                    cd ../potts_pamc
                    sh ./run.sh
                    ;;
-        ActiveLearn ) cd tests/integration/active_learn
-                      sh ./install_aenet.sh
-                      sh ./run.sh ;;
+        ActiveLearnAenet ) cd tests/integration/active_learn_aenet
+                            sh ./install_aenet.sh
+                            sh ./run.sh ;;
+        ActiveLearnNequip ) cd tests/integration/active_learn_nequip
+                             sh ./install_nequip.sh
+                             sh ./run.sh ;;
+        ActiveLearnMLIP-3 ) cd tests/integration/active_learn_mlip3
+                             sh ./install_mlip3.sh
+                             sh ./run.sh ;;
         * ) echo "Unknown testname";;
         esac
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
@@ -4,14 +4,14 @@ on: [push]
 
 jobs:
   check-build-doc:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     timeout-minutes: 10
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 

diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
@@ -12,24 +12,24 @@ on:
 jobs:
   deploy:
     timeout-minutes: 10.0
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Inject slug/short variables
       uses: rlespinasse/[email protected]
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: main
 
     - name: Checkout gh-pages
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: gh-pages
         path: gh-pages
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 

diff --git a/.github/workflows/deploy_pypi.yml b/.github/workflows/deploy_pypi.yml
@@ -6,13 +6,13 @@ on:
 
 jobs:
   deploy:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 

diff --git a/README.md b/README.md
@@ -9,13 +9,13 @@ and OpenMX input files for obtaining the reference training data for the machine
 
 ## Requirement
 
-- python3 (>=3.7)
+- python3 (>=3.9)
 - numpy
 - scipy
 - toml (for parsing input files)
 - mpi4py (for parallel tempering)
   - This requires one of the MPI implementation
-- pymatgen (>=2019.12.3) (for using Structure as a configuration)
+- pymatgen (>=2022.1.20) (for using Structure as a configuration)
   - This requires Cython
 - qe-tools (for parsing QE I/O)
 
@@ -25,7 +25,7 @@ Pymatgen requires Cython but Cython will not be installed automatically,
 please make sure that this is installed,
 
 ``` bash
-$ pip3 install Cython
+$ python3 -m pip install Cython
 ```
 
 mpi4py requires one of the MPI implementations such as OpenMPI,
@@ -39,7 +39,7 @@ $ brew install open-mpi
 After installing Cython and MPI,
 
 ``` bash
-$ pip3 install abics
+$ python3 -m pip install abics
 ```
 
 will install abICS and dependencies.
@@ -48,10 +48,10 @@ If you want to change the directory where abICS is installed,
 add `--user` option or `--prefix=DIRECTORY` option to the above command as
 
 ``` bash
-$ pip3 install --user abics
+$ python3 -m pip install --user abics
 ```
 
-For details of `pip` , see the manual of `pip` by `pip3 help install`
+For details of `pip` , see the manual of `pip` by `python3 -m pip help install`
 
 If you want to install abICS from source, see [wiki page](https://github.com/issp-center-dev/abICS/wiki/Install)
 
@@ -93,6 +93,6 @@ Shusuke Kasamatsu, Yuichi Motoyama, Tatsumi Aoyama, Kazuyoshi Yoshimi
 
 [English online manual](https://issp-center-dev.github.io/abICS/docs/master/en/html/index.html)
 
-[Japnese online manual](https://issp-center-dev.github.io/abICS/docs/master/ja/html/index.html)
+[Japanese online manual](https://issp-center-dev.github.io/abICS/docs/master/ja/html/index.html)
 
 [API reference](https://issp-center-dev.github.io/abICS/docs/api/master/html/index.html)
diff --git a/abics/__init__.py b/abics/__init__.py
@@ -1 +1 @@
-__version__ = "2.1.0"
+__version__ = "2.2.0"
diff --git a/abics/applications/latgas_abinitio_interface/__init__.py b/abics/applications/latgas_abinitio_interface/__init__.py
@@ -14,13 +14,19 @@
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see http://www.gnu.org/licenses/.
 
-# from .default_observer import *
 from .map2perflat import *
-from .aenet_trainer import *
 
-from .vasp import VASPSolver
-from .qe import QESolver
-from .aenet import AenetSolver
-from .aenet_pylammps import AenetPyLammpsSolver
-from .openmx import OpenMXSolver
-from .user_function_solver import UserFunctionSolver
+from .base_solver import register_solver
+from .base_trainer import register_trainer
+
+register_solver("vasp", "VASPSolver", "abics.applications.latgas_abinitio_interface.vasp")
+register_solver("qe", "QESolver", "abics.applications.latgas_abinitio_interface.qe")
+register_solver("openmx", "OpenMXSolver", "abics.applications.latgas_abinitio_interface.openmx")
+register_solver("aenet", "AenetSolver", "abics.applications.latgas_abinitio_interface.aenet")
+register_solver("nequip", "NequipSolver", "abics.applications.latgas_abinitio_interface.nequip")
+register_solver("mlip_3", "MLIP3Solver", "abics.applications.latgas_abinitio_interface.mlip_3")
+register_solver("User", "UserFunctionSolver", "abics.applications.latgas_abinitio_interface.user_function_solver")
+
+register_trainer("aenet", "AenetTrainer", "abics.applications.latgas_abinitio_interface.aenet_trainer")
+register_trainer("nequip", "NequipTrainer", "abics.applications.latgas_abinitio_interface.nequip_trainer")
+register_trainer("mlip_3", "MLIP3Trainer", "abics.applications.latgas_abinitio_interface.mlip_3_trainer")
diff --git a/abics/applications/latgas_abinitio_interface/aenet.py b/abics/applications/latgas_abinitio_interface/aenet.py
@@ -14,12 +14,6 @@
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see http://www.gnu.org/licenses/.
 
-"""
-Adapted from pymatgen.io.xcrysden distributed under the MIT License
-# Copyright (c) Pymatgen Development Team.
-# Distributed under the terms of the MIT License.
-"""
-
 from __future__ import annotations
 
 import os
@@ -28,105 +22,9 @@
 import numpy as np
 from pymatgen.core import Structure
 
-from .base_solver import SolverBase, register_solver
+from .base_solver import SolverBase
 from .params import ALParams, DFTParams
-
-
-def to_XSF(structure: Structure, write_force_zero=False):
-    """
-    Returns a string with the structure in XSF format
-    See http://www.xcrysden.org/doc/XSF.html
-    """
-    lines = []
-    app = lines.append
-
-    app("CRYSTAL")
-    app("# Primitive lattice vectors in Angstrom")
-    app("PRIMVEC")
-    cell = structure.lattice.matrix
-    for i in range(3):
-        app(" %.14f %.14f %.14f" % tuple(cell[i]))
-
-    cart_coords = structure.cart_coords
-    app("# Cartesian coordinates in Angstrom.")
-    app("PRIMCOORD")
-    app(" %d 1" % len(cart_coords))
-    species = structure.species
-    site_properties = structure.site_properties
-    if "forces" not in site_properties.keys():
-        write_force_zero = True
-    else:
-        forces = site_properties["forces"]
-
-    if write_force_zero:
-        for a in range(len(cart_coords)):
-            app(
-                str(species[a])
-                + " %20.14f %20.14f %20.14f" % tuple(cart_coords[a])
-                + " 0.0 0.0 0.0"
-            )
-    else:
-        for a in range(len(cart_coords)):
-            app(
-                str(species[a])
-                + " %20.14f %20.14f %20.14f" % tuple(cart_coords[a])
-                + " %20.14f %20.14f %20.14f" % tuple(forces[a])
-            )
-
-    return "\n".join(lines)
-
-
-def from_XSF(input_string: str):
-    """
-    Initialize a `Structure` object from a string with data in XSF format.
-
-    Args:
-        input_string: String with the structure in XSF format.
-            See http://www.xcrysden.org/doc/XSF.html
-        cls_: Structure class to be created. default: pymatgen structure
-
-    """
-    # CRYSTAL                                        see (1)
-    # these are primitive lattice vectors (in Angstroms)
-    # PRIMVEC
-    #    0.0000000    2.7100000    2.7100000         see (2)
-    #    2.7100000    0.0000000    2.7100000
-    #    2.7100000    2.7100000    0.0000000
-
-    # these are conventional lattice vectors (in Angstroms)
-    # CONVVEC
-    #    5.4200000    0.0000000    0.0000000         see (3)
-    #    0.0000000    5.4200000    0.0000000
-    #    0.0000000    0.0000000    5.4200000
-
-    # these are atomic coordinates in a primitive unit cell  (in Angstroms)
-    # PRIMCOORD
-    # 2 1                                            see (4)
-    # 16      0.0000000     0.0000000     0.0000000  see (5)
-    # 30      1.3550000    -1.3550000    -1.3550000
-
-    lattice, coords, species = [], [], []
-    lines = input_string.splitlines()
-
-    for i in range(len(lines)):
-        if "PRIMVEC" in lines[i]:
-            for j in range(i + 1, i + 4):
-                lattice.append([float(c) for c in lines[j].split()])
-
-        if "PRIMCOORD" in lines[i]:
-            num_sites = int(lines[i + 1].split()[0])
-
-            for j in range(i + 2, i + 2 + num_sites):
-                tokens = lines[j].split()
-                species.append(tokens[0])
-                coords.append([float(j) for j in tokens[1:4]])
-            break
-    else:
-        raise ValueError("Invalid XSF data")
-
-    s = Structure(lattice, species, coords, coords_are_cartesian=True)
-    return s
-
+from .util import structure_to_XSF, structure_from_XSF
 
 class AenetSolver(SolverBase):
     """
@@ -183,7 +81,7 @@ def update_info_by_structure(self, structure: Structure):
             if self.ignore_species is not None:
                 structure = structure.copy()
                 structure.remove_species(self.ignore_species)
-            self.pos_info = to_XSF(structure)
+            self.pos_info = structure_to_XSF(structure)
 
         def update_info_from_files(self, output_dir, rerun):
             """
@@ -262,7 +160,7 @@ def get_results(self, output_dir):
             # Read results from files in output_dir and calculate values
             Phys = namedtuple("PhysValues", ("energy", "structure"))
             with open(os.path.join(output_dir, "structure.xsf")) as f:
-                structure = from_XSF(f.read())
+                structure = structure_from_XSF(f.read())
             with open(os.path.join(output_dir, "stdout")) as f:
                 lines = f.read()
                 fi_io = io.StringIO(lines)
@@ -291,5 +189,3 @@ def create(cls, params: ALParams | DFTParams):
         ignore_species = params.ignore_species
         run_scheme = params.solver_run_scheme
         return cls(path, ignore_species, run_scheme)
-
-register_solver("aenet", AenetSolver)
diff --git a/abics/applications/latgas_abinitio_interface/aenet_pylammps.py b/abics/applications/latgas_abinitio_interface/aenet_pylammps.py
@@ -25,7 +25,7 @@
 import numpy as np
 from pymatgen.core import Structure
 
-from .base_solver import SolverBase, register_solver
+from .base_solver import SolverBase
 from .params import ALParams, DFTParams
 
 
@@ -62,7 +62,9 @@ def __init__(self, ignore_species):
         self.calc = lammps(
             cmdargs=["-log", "none", "-screen", "none", "-nocite"], comm=MPI.COMM_SELF
         )
-
+        self.rank = MPI.COMM_WORLD.Get_rank()
+
+        # debug             cmdargs=["-log", "test{}.log".format(MPI.COMM_WORLD.Get_rank()), "-screen", "none", "-nocite"], comm=MPI.COMM_SELF
     def name(self):
         return "aenetPyLammps"
 
@@ -77,21 +79,22 @@ def calculate_energy(self, fi, output_dir):
         latt = st.lattice.matrix
         ax = np.linalg.norm(latt[0])
         bx = np.dot(latt[1], unit_vec(latt[0]))
-        by = np.linalg.norm(np.outer(unit_vec(latt[0]), latt[1]))
+        by = np.linalg.norm(np.cross(unit_vec(latt[0]), latt[1]))
         cx = np.dot(latt[2], unit_vec(latt[0]))
         cy = (np.dot(latt[1], latt[2]) - bx * cx) / by
         cz = np.sqrt(np.linalg.norm(latt[2]) ** 2.0 - cx ** 2.0 - cy ** 2.0)
 
         # lmp = lammps(cmdargs=["-log", "none","-nocite"])
-
         self.calc.command("atom_style atomic")
         self.calc.command("units metal")
         self.calc.command("boundary p p p")
 
         self.calc.command(f"region box prism 0 {ax} 0 {by} 0 {cz} {bx} {cx} {cy}")
         self.calc.command(f"create_box {nspec} box")
         types = list(map(lambda x: spec_dict[x.name], st.species))
-        self.calc.create_atoms(natoms, None, types, st.cart_coords.ravel())
+        new_coords = np.dot(st.frac_coords, np.array([[ax,0,0], [bx,by,0], [cx,cy,cz]]))
+        self.calc.create_atoms(natoms, None, types, new_coords.ravel())
+
         for i in range(1, nspec + 1):
             self.calc.command(f"mass {i} 1")
         self.calc.commands_list(self.input.pair_pot)
@@ -224,6 +227,3 @@ def solver_run_schemes(self):
     def create(cls, params: ALParams | DFTParams):
         ignore_species = params.ignore_species
         return cls(ignore_species)
-
-
-register_solver("aenetpylammps", AenetPyLammpsSolver)