Merge branch 'update.algorithm.restart' into update.algorithm

doc/en/source/algorithm/bayes.rst

@@ -139,11 +139,11 @@ At each step of the optimization process, the values of the parameters and the c
 
 Restart
 ~~~~~~~~~~~~~~~~~~~~~~
-The execution mode is specified by the ``run_mode`` parameter to the ``Algorithm.main()`` method.
+The execution mode is specified by the ``run_mode`` parameter to the constructor.
 The operation of each mode is described as follows.
 The parameter values correspond to ``--init``, ``--resume``, and ``--cont`` options of ``py2dmat`` command, respectively.
 
-- ``"initialize"`` (default)
+- ``"initial"`` (default)
 
   The program is started from the initial state.
   First, it performs the random sampling for the number of times specified by ``random_max_num_probes`` parameter.

doc/en/source/algorithm/exchange.rst

@@ -243,11 +243,11 @@ The remaining columns are the coordinates.
 
 Restart
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The execution mode is specified by the ``run_mode`` parameter to the ``Algorithm.main()`` method.
+The execution mode is specified by the ``run_mode`` parameter to the constructor.
 The operation of each mode is described as follows.
 The parameter values correspond to ``--init``, ``--resume``, and ``--cont`` options of ``py2dmat`` command, respectively.
 
-- ``"initialize"`` (default)
+- ``"initial"`` (default)
 
   The program is started from the initialized state.
   If the checkpointing is enabled, the intermediate states will be stored at the folloing occasions:

doc/en/source/algorithm/mapper_mpi.rst

@@ -106,11 +106,11 @@ Below, output example is shown.
 
 Restart
 ~~~~~~~~~~~~~~~~~~~~~~
-The execution mode is specified by the ``run_mode`` parameter to the ``Algorithm.main()`` method.
+The execution mode is specified by the ``run_mode`` parameter to the constructor.
 The operation of each mode is described as follows.
 The parameter values correspond to ``--init``, ``--resume``, and ``--cont`` options of ``py2dmat`` command, respectively.
 
-- ``"initialize"`` (default)
+- ``"initial"`` (default)
 
   The program is started from the initial state.
   If the checkpointing is enabled, the intermediate states will be stored at the folloing occasions:

doc/en/source/algorithm/pamc.rst

@@ -296,11 +296,11 @@ The sixth column is the acceptance ratio of MC updates.
 
 Restart
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The execution mode is specified by the ``run_mode`` parameter to the ``Algorithm.main()`` method.
+The execution mode is specified by the ``run_mode`` parameter to the constructor.
 The operation of each mode is described as follows.
 The parameter values correspond to ``--init``, ``--resume``, and ``--cont`` options of ``py2dmat`` command, respectively.
 
-- ``"initialize"`` (default)
+- ``"initial"`` (default)
 
   The program is started from the initialized state.
   If the checkpointing is enabled, the intermediate states will be stored at the folloing occasions:

doc/ja/source/algorithm/bayes.rst

@@ -140,11 +140,11 @@
 
 リスタート
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``Algorithm.main()`` メソッドの引数 ``run_mode`` に実行モードを指定します。
+コンストラクタの引数 ``run_mode`` に実行モードを指定します。
 以下はそれぞれ ``py2dmat`` コマンドの引数の ``--init``, ``--resume``, ``--cont`` に対応します。
 各モードの動作は次のとおりです。
 
-- ``"initialize"`` (デフォルト)
+- ``"initial"`` (デフォルト)
 
   初期化して実行します。
   まず、ランダムサンプリングを ``random_max_num_probes`` に指定した回数だけ行います。

doc/ja/source/algorithm/exchange.rst

@@ -233,11 +233,11 @@ MPI並列を利用する場合は、あらかじめ `mpi4py <https://mpi4py.read
 
 リスタート
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``Algorithm.main()`` メソッドの引数 ``run_mode`` に実行モードを指定します。
+コンストラクタの引数 ``run_mode`` に実行モードを指定します。
 以下はそれぞれ ``py2dmat`` コマンドの引数の ``--init``, ``--resume``, ``--cont`` に対応します。
 各モードの動作は次のとおりです。
 
-- ``"initialize"`` (デフォルト)
+- ``"initial"`` (デフォルト)
 
   初期化して実行します。
   チェックポイント機能が有効な場合、以下のタイミングで実行時の状態をファイルに出力します。

doc/ja/source/algorithm/mapper_mpi.rst

@@ -109,11 +109,11 @@ MPI 並列を行う場合は、 `mpi4py <https://mpi4py.readthedocs.io/en/stable
 
 リスタート
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``Algorithm.main()`` メソッドの引数 ``run_mode`` に実行モードを指定します。
+コンストラクタの引数 ``run_mode`` に実行モードを指定します。
 以下はそれぞれ ``py2dmat`` コマンドの引数の ``--init``, ``--resume``, ``--cont`` に対応します。
 各モードの動作は次のとおりです。
 
-- ``"initialize"`` (デフォルト)
+- ``"initial"`` (デフォルト)
 
   初期化して実行します。
   チェックポイント機能が有効な場合、以下のタイミングで実行時の状態をファイルに出力します。

doc/ja/source/algorithm/pamc.rst

@@ -290,11 +290,11 @@ MPI 並列をする場合にはあらかじめ `mpi4py <https://mpi4py.readthedo
 
 リスタート
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``Algorithm.main()`` メソッドの引数 ``run_mode`` に実行モードを指定します。
+コンストラクタの引数 ``run_mode`` に実行モードを指定します。
 以下はそれぞれ ``py2dmat`` コマンドの引数の ``--init``, ``--resume``, ``--cont`` に対応します。
 各モードの動作は次のとおりです。
 
-- ``"initialize"`` (デフォルト)
+- ``"initial"`` (デフォルト)
 
   初期化して実行します。
   チェックポイント機能が有効な場合、以下のタイミングで実行時の状態をファイルに出力します。

src/py2dmat/_main.py

@@ -105,5 +105,5 @@ def main():
 
     solver = Solver(info)
     runner = py2dmat.Runner(solver, info)
-    alg = Algorithm(info, runner)
-    alg.main(run_mode=run_mode)
+    alg = Algorithm(info, runner, run_mode=run_mode)
+    result = alg.main()

src/py2dmat/algorithm/_algorithm.py

@@ -65,15 +65,18 @@ class AlgorithmBase(metaclass=ABCMeta):
 
     @abstractmethod
     def __init__(
-        self, info: py2dmat.Info, runner: Optional[py2dmat.Runner] = None
+            self,
+            info: py2dmat.Info,
+            runner: Optional[py2dmat.Runner] = None,
+            run_mode: str = "initial"
     ) -> None:
         self.mpicomm = mpi.comm()
         self.mpisize = mpi.size()
         self.mpirank = mpi.rank()
         self.timer = {"init": {}, "prepare": {}, "run": {}, "post": {}}
         self.timer["init"]["total"] = 0.0
         self.status = AlgorithmStatus.INIT
-        self.mode = None
+        self.mode = run_mode.lower()
 
         # keep copy of parameters
         self.info = copy.deepcopy(info.algorithm)
@@ -168,9 +171,7 @@ def post(self) -> Dict:
     def _post(self) -> Dict:
         pass
 
-    def main(self, run_mode: str = "initialize"):
-        self.mode = run_mode.lower()
-
+    def main(self):
         time_sta = time.perf_counter()
         self.prepare()
         time_end = time.perf_counter()

src/py2dmat/algorithm/bayes.py

@@ -48,8 +48,10 @@ class Algorithm(py2dmat.algorithm.AlgorithmBase):
 
     def __init__(self, info: py2dmat.Info,
                  runner: py2dmat.Runner = None,
-                 domain = None) -> None:
-        super().__init__(info=info, runner=runner)
+                 domain = None,
+                 run_mode: str = "initial"
+    ) -> None:
+        super().__init__(info=info, runner=runner, run_mode=run_mode)
 
         info_param = info.algorithm.get("param", {})
         info_bayes = info.algorithm.get("bayes", {})

src/py2dmat/algorithm/exchange.py

@@ -75,13 +75,17 @@ class Algorithm(py2dmat.algorithm.montecarlo.AlgorithmBase):
 
     exchange_direction: bool
 
-    def __init__(self, info: py2dmat.Info, runner: py2dmat.Runner = None) -> None:
+    def __init__(self,
+                 info: py2dmat.Info,
+                 runner: py2dmat.Runner = None,
+                 run_mode: str = "initial"
+    ) -> None:
         time_sta = time.perf_counter()
 
         info_exchange = info.algorithm["exchange"]
         nwalkers = info_exchange.get("nreplica_per_proc", 1)
 
-        super().__init__(info=info, runner=runner, nwalkers=nwalkers)
+        super().__init__(info=info, runner=runner, nwalkers=nwalkers, run_mode=run_mode)
 
         self.nreplica = self.mpisize * self.nwalkers
         self.input_as_beta, self.betas = read_Ts(info_exchange, numT=self.nreplica)

src/py2dmat/algorithm/mapper_mpi.py

@@ -30,8 +30,10 @@ class Algorithm(py2dmat.algorithm.AlgorithmBase):
 
     def __init__(self, info: py2dmat.Info,
                  runner: py2dmat.Runner = None,
-                 domain = None) -> None:
-        super().__init__(info=info, runner=runner)
+                 domain = None,
+                 run_mode: str = "initial"
+    ) -> None:
+        super().__init__(info=info, runner=runner, run_mode=run_mode)
 
         if domain and isinstance(domain, py2dmat.domain.MeshGrid):
             self.domain = domain

src/py2dmat/algorithm/min_search.py

@@ -51,8 +51,10 @@ class Algorithm(py2dmat.algorithm.AlgorithmBase):
 
     def __init__(self, info: py2dmat.Info,
                  runner: py2dmat.Runner = None,
-                 domain = None) -> None:
-        super().__init__(info=info, runner=runner)
+                 domain = None,
+                 run_mode: str = "initial"
+    ) -> None:
+        super().__init__(info=info, runner=runner, run_mode=run_mode)
 
         if domain and isinstance(domain, py2dmat.domain.Region):
             self.domain = domain

src/py2dmat/algorithm/montecarlo.py

@@ -95,10 +95,11 @@ class AlgorithmBase(py2dmat.algorithm.AlgorithmBase):
     def __init__(self, info: py2dmat.Info,
                  runner: py2dmat.Runner = None,
                  domain = None,
-                 nwalkers: int = 1
+                 nwalkers: int = 1,
+                 run_mode: str = "initial"
     ) -> None:
         time_sta = time.perf_counter()
-        super().__init__(info=info, runner=runner)
+        super().__init__(info=info, runner=runner, run_mode=run_mode)
         self.nwalkers = nwalkers
 
         if domain:

src/py2dmat/algorithm/pamc.py

@@ -94,13 +94,17 @@ class Algorithm(py2dmat.algorithm.montecarlo.AlgorithmBase):
     Fmeans: np.ndarray
     Ferrs: np.ndarray
 
-    def __init__(self, info: py2dmat.Info, runner: py2dmat.Runner = None) -> None:
+    def __init__(self,
+                 info: py2dmat.Info,
+                 runner: py2dmat.Runner = None,
+                 run_mode: str = "initial"
+    ) -> None:
         time_sta = time.perf_counter()
 
         info_pamc = info.algorithm["pamc"]
         nwalkers = info_pamc.get("nreplica_per_proc", 1)
 
-        super().__init__(info=info, runner=runner, nwalkers=nwalkers)
+        super().__init__(info=info, runner=runner, nwalkers=nwalkers, run_mode=run_mode)
 
         self.verbose = True and self.mpirank == 0