Merge branch 'update.solver_module' into update

extra/leed/README.md

@@ -0,0 +1 @@
+# LEED solver module for Py2DMAT

extra/leed/pyproject.toml

@@ -0,0 +1,36 @@
+[tool.poetry]
+name = "leed"
+version = "1.0-dev"
+description = "LEED solver module for Py2DMAT: data-analysis software of quantum beam diffraction experiments for 2D material structure"
+authors = ["2DMAT developers <[email protected]>"]
+license = "GPL-3.0-or-later"
+
+readme = "README.md"
+repository = "https://github.com/issp-center-dev/py2dmat-leed"
+
+packages = [
+  { include = "leed", from = "src" }
+  ]
+
+[tool.poetry.dependencies]
+python = ">=3.6.8"
+numpy = "^1.14"
+#mpi4py = {version = "^3", optional = true}
+py2dmat = "^2"
+
+#[tool.poetry.extras]
+#min_search = ["scipy"]
+#bayes = ["physbo"]
+#exchange = ["mpi4py"]
+#all = ["scipy", "mpi4py", "physbo"]
+
+#[tool.poetry.dev-dependencies]
+#black = "^22.3.0"
+#pynvim = "^0.4.3"
+
+[tool.poetry.scripts]
+py2dmat-leed = "leed._main:main"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

extra/leed/src/leed/__init__.py

@@ -0,0 +1,3 @@
+from .leed import Solver
+
+__version__ = "1.0-dev"

extra/leed/src/leed/_main.py

@@ -0,0 +1,68 @@
+# 2DMAT -- Data-analysis software of quantum beam diffraction experiments for 2D material structure
+# Copyright (C) 2020- 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/.
+
+from sys import exit
+
+import py2dmat
+import py2dmat.mpi
+import py2dmat.util.toml
+
+from leed import Solver
+
+def main():
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description=(
+            "Data-analysis software of quantum beam "
+            "diffraction experiments for 2D material structure"
+        )
+    )
+    parser.add_argument("inputfile", help="input file with TOML format")
+    parser.add_argument("--version", action="version", version=py2dmat.__version__)
+
+    args = parser.parse_args()
+
+    file_name = args.inputfile
+    inp = {}
+    if py2dmat.mpi.rank() == 0:
+        inp = py2dmat.util.toml.load(file_name)
+    if py2dmat.mpi.size() > 1:
+        inp = py2dmat.mpi.comm().bcast(inp, root=0)
+    info = py2dmat.Info(inp)
+
+    algname = info.algorithm["name"]
+    if algname == "mapper":
+        from py2dmat.algorithm.mapper_mpi import Algorithm
+    elif algname == "minsearch":
+        from py2dmat.algorithm.min_search import Algorithm
+    elif algname == "exchange":
+        from py2dmat.algorithm.exchange import Algorithm
+    elif algname == "pamc":
+        from py2dmat.algorithm.pamc import Algorithm
+    elif algname == "bayes":
+        from py2dmat.algorithm.bayes import Algorithm
+    else:
+        print(f"ERROR: Unknown algorithm ({algname})")
+        exit(1)
+
+    solver = Solver(info)
+    runner = py2dmat.Runner(solver, info)
+    alg = Algorithm(info, runner)
+    alg.main()
+
+if __name__ == "__main__":
+    main()

src/py2dmat/solver/leed.py → extra/leed/src/leed/leed.py

@@ -14,27 +14,49 @@
 # 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 typing import List
+from typing import Dict, List
 import itertools
 import os
 import os.path
 import shutil
 from distutils.dir_util import copy_tree
 from pathlib import Path
+import subprocess
 
 import numpy as np
 
 import py2dmat
 from py2dmat import exception
 
 
-class Solver(py2dmat.solver.SolverBase):
+class Solver:
+    #-----
+    root_dir: Path
+    output_dir: Path
+    proc_dir: Path
+    work_dir: Path
+    _name: str
+    dimension: int
+    timer: Dict[str, Dict]
+    #-----
     path_to_solver: Path
 
     dimension: int
 
     def __init__(self, info: py2dmat.Info):
-        super().__init__(info)
+        #-----
+        #super().__init__(info)
+        self.root_dir = info.base["root_dir"]
+        self.output_dir = info.base["output_dir"]
+        self.proc_dir = self.output_dir / str(py2dmat.mpi.rank())
+        self.work_dir = self.proc_dir
+        self._name = ""
+        self.timer = {"prepare": {}, "run": {}, "post": {}}
+        if "dimension" in info.solver:
+            self.dimension = info.solver["dimension"]
+        else:
+            self.dimension = info.base["dimension"]
+        #-----
 
         self._name = "leed"
         info_s = info.solver
@@ -80,6 +102,10 @@ def check_keywords(key, segment, registered_list):
                 )
         self.input = Solver.Input(info)
 
+    @property
+    def name(self) -> str:
+        return self._name
+
     def prepare(self, message: py2dmat.Message) -> None:
         self.work_dir = self.proc_dir
         for dir in [self.path_to_base_dir]:
@@ -89,6 +115,15 @@ def prepare(self, message: py2dmat.Message) -> None:
     def run(self, nprocs: int = 1, nthreads: int = 1) -> None:
         self._run_by_subprocess([str(self.path_to_solver)])
 
+    def _run_by_subprocess(self, command: List[str]) -> None:
+        with open("stdout", "w") as fi:
+            subprocess.run(
+                command,
+                stdout=fi,
+                stderr=subprocess.STDOUT,
+                check=True,
+            )
+
     def get_results(self) -> float:
         # Get R-factor
         rfactor = -1.0