update tutorials (fix file paths)

doc/en/source/tutorial/bayes.rst

@@ -7,7 +7,7 @@ This tutorial subscribes how to estimate atomic positions from the experimental
 Sample files
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-Sample files are available from ``sample/sim-trhepd-rheed/bayes`` .
+Sample files are available from ``sample/sim-trhepd-rheed/single_beam/bayes`` .
 This directory includes the following files:
 
 - ``bulk.txt``
@@ -123,14 +123,14 @@ First, move to the folder where the sample file is located (hereinafter, it is a
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/bayes
+    cd sample/sim-trhepd-rheed/single_beam/bayes
 
 Copy ``bulk.exe`` and ``surf.exe`` as the tutorial for the direct problem.
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 Execute ``bulk.exe`` to generate ``bulkP.b`` .
 
@@ -142,7 +142,7 @@ Then, run the main program (it takes a few secondes)
 
 .. code-block::
 
-   python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+   python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 This makes a directory with the name of ``0`` .
 The following standard output will be shown:
@@ -216,7 +216,7 @@ I will omit the explanation below, but I will post the contents.
 
     ./bulk.exe
 
-    time python3 ../../../src/py2dmat_main.py input.toml
+    time python3 ../../../../src/py2dmat_main.py input.toml
 
     echo diff BayesData.txt ref_BayesData.txt
     res=0

doc/en/source/tutorial/exchange.rst

@@ -6,7 +6,7 @@ This tutorial subscribes how to estimate atomic positions from the experimental
 Sample files
 ~~~~~~~~~~~~~~~~~~
 
-Sample files are available from ``sample/sim-trhepd-rheed/exchange`` .
+Sample files are available from ``sample/sim-trhepd-rheed/single_beam/exchange`` .
 This directory includes the following files:
 
 - ``bulk.txt``
@@ -126,14 +126,14 @@ First, move to the folder where the sample file is located (hereinafter, it is a
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/exchange
+    cd sample/sim-trhepd-rheed/single_beam/exchange
 
 Copy ``bulk.exe`` and ``surf.exe`` as the tutorial for the direct problem.
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 Execute ``bulk.exe`` to generate ``bulkP.b`` .
 
@@ -145,7 +145,7 @@ Then, run the main program (it takes a few secondes)
 
 .. code-block::
 
-    mpiexec -np 4 python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+    mpiexec -np 4 python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 
 Here, the calculation is performed using MPI parallel with 4 processes.
@@ -187,7 +187,7 @@ I will omit the explanation below, but I will post the contents.
 
   ./bulk.exe
 
-  time mpiexec --oversubscribe -np 4 python3 ../../../src/py2dmat_main.py input.toml
+  time mpiexec --oversubscribe -np 4 python3 ../../../../src/py2dmat_main.py input.toml
 
   echo diff best_result.txt ref.txt
   res=0
@@ -207,7 +207,7 @@ The ``result.txt`` in each rank folder records the data sampled by each replica,
 
 .. code-block::
 
-  python3 ../../../script/separateT.py
+  python3 ../../../../script/separateT.py
 
 
 The data reorganized for each temperature point is written to ``result_T%.txt`` (``%`` is the index of the temperature point).

doc/en/source/tutorial/minsearch.rst

@@ -22,7 +22,7 @@ In the main program, the Nelder-Mead method (using `scipy.optimize.fmin <https:/
 Location of the sample files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The sample files are located in ``sample/py2dmat/sim-trhepd-rheed/minsearch``.
+The sample files are located in ``sample/py2dmat/sim-trhepd-rheed/single_beam/minsearch``.
 The following files are stored in the folder.
 
 - ``bulk.txt``
@@ -182,14 +182,14 @@ First, move to the folder where the sample files are located (we will assume tha
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/minsearch
+    cd sample/sim-trhepd-rheed/single_beam/minsearch
 
 Copy ``bulk.exe`` and ``surf.exe``.
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 First, run ``bulk.exe`` to create ``bulkP.b``.
 
@@ -201,7 +201,7 @@ After that, run the main program (the computation time takes only a few seconds
 
 .. code-block::
 
-    python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+    python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 Then, the standard output will be seen as follows.
 
@@ -250,7 +250,7 @@ Here is what it does, without further explanation.
 
   ./bulk.exe
 
-  time python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+  time python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
   echo diff res.txt ref.txt
   res=0
@@ -274,7 +274,7 @@ In this section, we will use this tool to visualize the results.
 
     cp 0/Log00000001_00000001/RockingCurve.txt RockingCurve_ini.txt
     cp 0/Log00000062_00000001/RockingCurve.txt RockingCurve_con.txt
-    cp ../../../script/draw_RC_double.py .
+    cp ../../../../script/draw_RC_double.py .
     python draw_RC_double.py
 
 Running the above will output ``RC_double.png``.

doc/en/source/tutorial/mpi.rst

@@ -8,7 +8,7 @@ However, it is necessary to prepare the data ``MeshData.txt`` to give the search
 Location of the sample files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The sample files are located in ``sample/sim-trhepd-rheed/mapper``.
+The sample files are located in ``sample/sim-trhepd-rheed/single_beam/mapper``.
 The following files are stored in the folder
 
 - ``bulk.txt``
@@ -139,14 +139,14 @@ First, move to the folder where the sample files are located (we will assume tha
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/minsearch
+    cd sample/sim-trhepd-rheed/single_beam/minsearch
 
 Copy ``bulk.exe`` and ``surf.exe``.
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 First, run ``bulk.exe`` to create ``bulkP.b``.
 
@@ -158,7 +158,7 @@ After that, run the main program (the computation time takes only a few seconds
 
 .. code-block::
 
-    mpiexec -np 2 python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+    mpiexec -np 2 python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 Here, the calculation using MPI parallel with 2 processes will be done.
 When executed, a folder for each rank will be created, and a subfolder ``Log%%%%%`` (where ``%%%%%`` is the grid id) will be created under it.
@@ -208,7 +208,7 @@ Here is what it does, without further explanation.
 
     ./bulk.exe
 
-    time mpiexec -np 2 python3 ../../../src/py2dmat_main.py input.toml
+    time mpiexec -np 2 python3 ../../../../src/py2dmat_main.py input.toml
 
     echo diff ColorMap.txt ref_ColorMap.txt
     res=0

doc/en/source/tutorial/pamc.rst

@@ -6,7 +6,7 @@ This tutorial subscribes how to estimate atomic positions from the experimental
 Sample files
 ~~~~~~~~~~~~~~~~~~
 
-Sample files are available from ``sample/sim-trhepd-rheed/pamc`` .
+Sample files are available from ``sample/sim-trhepd-rheed/single_beam/pamc`` .
 This directory includes the following files:
 
 - ``bulk.txt``
@@ -132,14 +132,14 @@ First, move to the folder where the sample file is located (hereinafter, it is a
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/pamc
+    cd sample/sim-trhepd-rheed/single_beam/pamc
 
 Copy ``bulk.exe`` and ``surf.exe`` as the tutorial for the direct problem.
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 Execute ``bulk.exe`` to generate ``bulkP.b`` .
 
@@ -151,7 +151,7 @@ Then, run the main program (it takes a few secondes)
 
 .. code-block::
 
-    mpiexec -np 4 python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+    mpiexec -np 4 python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 
 Here, the calculation is performed using MPI parallel with 4 processes.
@@ -217,7 +217,7 @@ I will omit the explanation below, but I will post the contents.
 
   ./bulk.exe
 
-  time mpiexec --oversubscribe -np 4 python3 ../../../src/py2dmat_main.py input.toml
+  time mpiexec --oversubscribe -np 4 python3 ../../../../src/py2dmat_main.py input.toml
 
   echo diff output/fx.txt ref.txt
   res=0

doc/ja/source/tutorial/bayes.rst

@@ -8,7 +8,7 @@
 サンプルファイルの場所
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-サンプルファイルは ``sample/sim-trhepd-rheed/bayes`` にあります。
+サンプルファイルは ``sample/sim-trhepd-rheed/single_beam/bayes`` にあります。
 フォルダには以下のファイルが格納されています。
 
 - ``bulk.txt``
@@ -166,8 +166,8 @@
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 最初に ``bulk.exe`` を実行し、 ``bulkP.b`` を作成します。
 
@@ -179,7 +179,7 @@
 
 .. code-block::
 
-   python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+   python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 実行すると、各ランクのフォルダが作成されます。
 以下の様な標準出力がされます。
@@ -255,7 +255,7 @@
 
     ./bulk.exe
 
-    time python3 ../../../src/py2dmat_main.py input.toml
+    time python3 ../../../../src/py2dmat_main.py input.toml
 
     echo diff BayesData.txt ref_BayesData.txt
     res=0

doc/ja/source/tutorial/exchange.rst

@@ -7,7 +7,7 @@
 サンプルファイルの場所
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-サンプルファイルは ``sample/sim-threpd-rheed/exchange`` にあります。
+サンプルファイルは ``sample/sim-threpd-rheed/single_beam/exchange`` にあります。
 フォルダには以下のファイルが格納されています。
 
 - ``bulk.txt``
@@ -116,14 +116,14 @@
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/exchange
+    cd sample/sim-trhepd-rheed/single_beam/exchange
 
 順問題の時と同様に、 ``bulk.exe`` と ``surf.exe`` をコピーします。
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 最初に ``bulk.exe`` を実行し、``bulkP.b`` を作成します。
 
@@ -135,7 +135,7 @@
 
 .. code-block::
 
-    mpiexec -np 4 python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+    mpiexec -np 4 python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 ここではプロセス数4のMPI並列を用いた計算を行っています。
 (Open MPI を用いる場合で、使えるコア数よりも要求プロセス数の方が多い時には、
@@ -177,7 +177,7 @@
 
   ./bulk.exe
 
-  time mpiexec --oversubscribe -np 4 python3 ../../../src/py2dmat_main.py input.toml
+  time mpiexec --oversubscribe -np 4 python3 ../../../../src/py2dmat_main.py input.toml
 
   echo diff best_result.txt ref.txt
   res=0
@@ -198,7 +198,7 @@ Py2DMat の実装では同一レプリカが様々な温度のサンプルを保
 
 .. code-block::
 
-  python3 ../../../script/separateT.py
+  python3 ../../../../script/separateT.py
 
 ``result_T%.txt`` に各温度点ごとにまとめなおされたデータが書き込まれます(``%`` は温度点のindex)。
 1列目がステップ、2列めがランク、3列目が目的関数の値、4列目以降がパラメータです。

doc/ja/source/tutorial/minsearch.rst

@@ -24,7 +24,7 @@ Nelder-Mead法 (`scipy.optimize.fmin <https://docs.scipy.org/doc/scipy/reference
 サンプルファイルの場所
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-サンプルファイルは ``sample/py2dmat/sim-threpd-rheed/minsearch`` にあります。
+サンプルファイルは ``sample/py2dmat/sim-threpd-rheed/single_beam/minsearch`` にあります。
 フォルダには以下のファイルが格納されています。
 
 - ``bulk.txt``
@@ -187,14 +187,14 @@ Nelder-Mead法 (`scipy.optimize.fmin <https://docs.scipy.org/doc/scipy/reference
 
 .. code-block::
 
-    cd sample/sim-trhepd-rheed/minsearch
+    cd sample/sim-trhepd-rheed/single_beam/minsearch
 
 順問題の時と同様に、``bulk.exe`` と ``surf.exe`` をコピーします。
 
 .. code-block::
 
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
-    cp ../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/bulk.exe .
+    cp ../../../../../sim-trhepd-rheed/src/TRHEPD/surf.exe .
 
 最初に ``bulk.exe`` を実行し、``bulkP.b`` を作成します。
 
@@ -206,7 +206,7 @@ Nelder-Mead法 (`scipy.optimize.fmin <https://docs.scipy.org/doc/scipy/reference
 
 .. code-block::
 
-    python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+    python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
 実行すると、以下の様な出力がされます。
 
@@ -254,7 +254,7 @@ Nelder-Mead法 (`scipy.optimize.fmin <https://docs.scipy.org/doc/scipy/reference
 
   ./bulk.exe
 
-  time python3 ../../../src/py2dmat_main.py input.toml | tee log.txt
+  time python3 ../../../../src/py2dmat_main.py input.toml | tee log.txt
 
   echo diff res.txt ref.txt
   res=0
@@ -278,7 +278,7 @@ Nelder-Mead法 (`scipy.optimize.fmin <https://docs.scipy.org/doc/scipy/reference
 
     cp 0/Log00000001_00000001/RockingCurve.txt RockingCurve_ini.txt
     cp 0/Log00000062_00000001/RockingCurve.txt RockingCurve_con.txt
-    cp ../../../script/draw_RC_double.py .
+    cp ../../../../script/draw_RC_double.py .
     python draw_RC_double.py
 
 上記を実行することで、``RC_double.png`` が出力されます。