restore aenetPyLammps

abics/applications/latgas_abinitio_interface/__init__.py

@@ -23,6 +23,7 @@
 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("aenetPyLammps", "AenetPyLammpsSolver", "abics.applications.latgas_abinitio_interface.aenet_pylammps")
 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")

abics/applications/latgas_abinitio_interface/aenet.py

@@ -26,12 +26,15 @@
 from .params import ALParams, DFTParams
 from .util import structure_to_XSF, structure_from_XSF
 
+
 class AenetSolver(SolverBase):
     """
     This class defines the aenet solver.
     """
 
-    def __init__(self, path_to_solver: os.PathLike, ignore_species=None, run_scheme="subprocess"):
+    def __init__(
+        self, path_to_solver: os.PathLike, ignore_species=None, run_scheme="subprocess"
+    ):
         """
         Initialize the solver.
 
@@ -49,7 +52,7 @@ def name(self):
         return "aenet"
 
     class Input(object):
-        def __init__(self, ignore_species : str | None, run_scheme="subprocess"):
+        def __init__(self, ignore_species: str | None, run_scheme="subprocess"):
             self.base_info = None
             self.pos_info = None
             self.ignore_species = ignore_species
@@ -138,6 +141,8 @@ def cl_args(self, nprocs, nthreads, output_dir):
                     os.path.join(output_dir, "predict.in"),
                     os.path.join(output_dir, "structure.xsf"),
                 ]
+            else:
+                raise RuntimeError("Invalid run_scheme: {}".format(self.run_scheme))
 
     class Output(object):
         def get_results(self, output_dir):

abics/applications/latgas_abinitio_interface/aenet_pylammps.py

@@ -63,8 +63,9 @@ def __init__(self, ignore_species):
             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"
 
@@ -82,7 +83,7 @@ def calculate_energy(self, fi, output_dir):
         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)
+        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")
@@ -92,9 +93,11 @@ def calculate_energy(self, fi, output_dir):
         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))
-        new_coords = np.dot(st.frac_coords, np.array([[ax,0,0], [bx,by,0], [cx,cy,cz]]))
+        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)

abics/applications/latgas_abinitio_interface/params.py

@@ -174,6 +174,7 @@ def from_toml(cls, f):
         d = toml.load(f)
         return cls.from_dict(d["mlref"]["solver"])
 
+
 class TrainerParams:
     def __init__(self):
         self.base_input_dir = []

tests/test_aenet.py

@@ -22,6 +22,8 @@
 
 from pymatgen.core import Structure
 
+from abics.applications.latgas_abinitio_interface.base_solver import create_solver
+from abics.applications.latgas_abinitio_interface.params import DFTParams
 from abics.applications.latgas_abinitio_interface.aenet import AenetSolver
 
 
@@ -35,11 +37,17 @@ def setUpClass(cls):
         os.makedirs(workdir)
 
     def setUp(self):
-        self.solver = AenetSolver(".")
+        params = DFTParams.from_dict(
+            {"type": "aenet", "path": ".", "run_scheme": "subprocess"}
+        )
+        self.solver = create_solver(params.solver, params)
         self.rootdir = os.path.dirname(__file__)
         self.datadir = os.path.join(self.rootdir, "data", "aenet")
         self.workdir = os.path.join(self.rootdir, "res", "aenet")
 
+    def test_create_solver(self):
+        self.assertIsInstance(self.solver, AenetSolver)
+
     def test_get_results(self):
         res = self.solver.output.get_results(self.datadir)
         res.structure.to("POSCAR", os.path.join(self.workdir, "pos.vasp"))
@@ -68,4 +76,10 @@ def test_cl_algs(self):
         nthreads = 4
         workdir = "work"
         res = self.solver.input.cl_args(nprocs, nthreads, workdir)
-        self.assertEqual(res, [os.path.join(workdir, "predict.in"), os.path.join(workdir, "structure.xsf")])
+        self.assertEqual(
+            res,
+            [
+                os.path.join(workdir, "predict.in"),
+                os.path.join(workdir, "structure.xsf"),
+            ],
+        )

tests/test_aenetpylammps.py

@@ -0,0 +1,57 @@
+# ab-Initio Configuration Sampling tool kit (abICS)
+# Copyright (C) 2019- The University of Tokyo
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see http://www.gnu.org/licenses/.
+
+import os
+import shutil
+import unittest
+
+import numpy as np
+
+from pymatgen.core import Structure
+
+from abics.applications.latgas_abinitio_interface.base_solver import create_solver
+from abics.applications.latgas_abinitio_interface.params import DFTParams
+from abics.applications.latgas_abinitio_interface.aenet_pylammps import (
+    AenetPyLammpsSolver,
+)
+
+
+class TestAenetPyLammps(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        rootdir = os.path.dirname(__file__)
+        workdir = os.path.join(rootdir, "res", "aenet")
+        if os.path.exists(workdir):
+            shutil.rmtree(workdir)
+        os.makedirs(workdir)
+
+    def setUp(self):
+        params = DFTParams.from_dict({"type": "aenetPyLammps", "path": "."})
+
+        self.imported = False
+        try:
+            self.solver = create_solver(params.solver, params)
+            self.imported = True
+        except ImportError:
+            self.imported = False
+
+        self.rootdir = os.path.dirname(__file__)
+        self.datadir = os.path.join(self.rootdir, "data", "aenet")
+        self.workdir = os.path.join(self.rootdir, "res", "aenet")
+
+    def test_create_solver(self):
+        if self.imported:
+            self.assertIsInstance(self.solver, AenetPyLammpsSolver)

tests/test_openmx.py

@@ -22,7 +22,12 @@
 
 from pymatgen.core import Structure
 
-from abics.applications.latgas_abinitio_interface.openmx import OpenMXInputFile, OpenMXSolver
+from abics.applications.latgas_abinitio_interface.base_solver import create_solver
+from abics.applications.latgas_abinitio_interface.params import DFTParams
+from abics.applications.latgas_abinitio_interface.openmx import (
+    OpenMXInputFile,
+    OpenMXSolver,
+)
 
 
 class TestOpenMX(unittest.TestCase):
@@ -38,7 +43,17 @@ def setUp(self):
         self.rootdir = os.path.dirname(__file__)
         self.datadir = os.path.join(self.rootdir, "data", "openmx")
         self.workdir = os.path.join(self.rootdir, "res", "openmx")
-        self.solver = OpenMXSolver(os.path.join(self.datadir, "bin", "openmx.dummy"))
+        params = DFTParams.from_dict(
+            {
+                "type": "openmx",
+                "path": os.path.join(self.datadir, "bin", "openmx.dummy"),
+                "run_scheme": "subprocess",
+            }
+        )
+        self.solver = create_solver(params.solver, params)
+
+    def test_create_solver(self):
+        self.assertIsInstance(self.solver, OpenMXSolver)
 
     def test_get_results(self):
         self.solver.input.from_directory(os.path.join(self.datadir, "baseinput"))
@@ -51,7 +66,7 @@ def test_get_results(self):
 
     def test_input(self):
         self.solver.input.from_directory(os.path.join(self.datadir, "baseinput"))
-        A = 4.0*np.eye(3)
+        A = 4.0 * np.eye(3)
         r = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
         st = Structure(
             A,
@@ -70,7 +85,6 @@ def test_input(self):
 
         self.assertEqual(res, ref)
 
-
     def test_cl_algs(self):
         self.solver.input.from_directory(os.path.join(self.datadir, "baseinput"))
         nprocs = 2

tests/test_qe.py

@@ -22,6 +22,8 @@
 
 from pymatgen.core import Structure
 
+from abics.applications.latgas_abinitio_interface.base_solver import create_solver
+from abics.applications.latgas_abinitio_interface.params import DFTParams
 from abics.applications.latgas_abinitio_interface.qe import QESolver
 
 from qe_tools.parsers import PwInputFile
@@ -37,11 +39,15 @@ def setUpClass(cls):
         os.makedirs(workdir)
 
     def setUp(self):
-        self.solver = QESolver(".")
+        params = DFTParams.from_dict({"type": "qe", "path": "."})
+        self.solver = create_solver(params.solver, params)
         self.rootdir = os.path.dirname(__file__)
         self.datadir = os.path.join(self.rootdir, "data", "qe")
         self.workdir = os.path.join(self.rootdir, "res", "qe")
 
+    def test_create_solver(self):
+        self.assertIsInstance(self.solver, QESolver)
+
     def test_get_results(self):
         res = self.solver.output.get_results(self.datadir)
         res.structure.to("POSCAR", os.path.join(self.workdir, "pos.vasp"))
@@ -52,7 +58,7 @@ def test_get_results(self):
 
     def test_input(self):
         self.solver.input.from_directory(os.path.join(self.datadir, "baseinput"))
-        A = 4.0*np.eye(3)
+        A = 4.0 * np.eye(3)
         r = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
         st = Structure(
             A,
@@ -72,15 +78,21 @@ def test_input(self):
 
         self.assertEqual(res.namelists, ref.namelists)
 
-        self.assertTrue(np.allclose(res.cell_parameters["cell"], ref.cell_parameters["cell"]))
-        self.assertTrue(np.allclose(res.atomic_positions["positions"], ref.atomic_positions["positions"]))
-        self.assertEqual(res.atomic_positions["fixed_coords"], ref.atomic_positions["fixed_coords"])
-
+        self.assertTrue(
+            np.allclose(res.cell_parameters["cell"], ref.cell_parameters["cell"])
+        )
+        self.assertTrue(
+            np.allclose(
+                res.atomic_positions["positions"], ref.atomic_positions["positions"]
+            )
+        )
+        self.assertEqual(
+            res.atomic_positions["fixed_coords"], ref.atomic_positions["fixed_coords"]
+        )
 
     def test_cl_algs(self):
         nprocs = 2
         nthreads = 4
         workdir = "work"
         res = self.solver.input.cl_args(nprocs, nthreads, workdir)
         self.assertEqual(res, ["-in", os.path.join(workdir, "scf.in")])
-

tests/test_vasp.py

@@ -23,6 +23,8 @@
 from pymatgen.core import Structure
 from pymatgen.io.vasp.inputs import VaspInput
 
+from abics.applications.latgas_abinitio_interface.base_solver import create_solver
+from abics.applications.latgas_abinitio_interface.params import DFTParams
 from abics.applications.latgas_abinitio_interface.vasp import VASPSolver
 
 
@@ -36,11 +38,15 @@ def setUpClass(cls):
         os.makedirs(workdir)
 
     def setUp(self):
-        self.solver = VASPSolver(".")
+        params = DFTParams.from_dict({"type": "vasp", "path": "."})
+        self.solver = create_solver(params.solver, params)
         self.rootdir = os.path.dirname(__file__)
         self.datadir = os.path.join(self.rootdir, "data", "vasp")
         self.workdir = os.path.join(self.rootdir, "res", "vasp")
 
+    def test_create_solver(self):
+        self.assertIsInstance(self.solver, VASPSolver)
+
     def test_get_results(self):
         os.utime(os.path.join(self.datadir, "output", "OSZICAR"))
         res = self.solver.output.get_results(os.path.join(self.datadir, "output"))
@@ -69,7 +75,7 @@ def test_input(self):
 
         self.assertEqual(res["INCAR"], ref["INCAR"])
         self.assertTrue(res["POSCAR"].structure.matches(ref["POSCAR"].structure))
-        for k,v in ref["POSCAR"].structure.site_properties.items():
+        for k, v in ref["POSCAR"].structure.site_properties.items():
             self.assertTrue(np.allclose(res["POSCAR"].structure.site_properties[k], v))
 
     def test_cl_algs(self):
@@ -78,4 +84,3 @@ def test_cl_algs(self):
         workdir = "work"
         res = self.solver.input.cl_args(nprocs, nthreads, workdir)
         self.assertEqual(res, [workdir])
-