From b17831d6e6b42bc612f09b317b5f24d79b27b229 Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Wed, 13 Mar 2024 14:21:19 +0900 Subject: [PATCH] update tutorials (fix file paths) --- doc/en/source/tutorial/bayes.rst | 12 ++++++------ doc/en/source/tutorial/exchange.rst | 14 +++++++------- doc/en/source/tutorial/minsearch.rst | 14 +++++++------- doc/en/source/tutorial/mpi.rst | 12 ++++++------ doc/en/source/tutorial/pamc.rst | 12 ++++++------ doc/ja/source/tutorial/bayes.rst | 10 +++++----- doc/ja/source/tutorial/exchange.rst | 14 +++++++------- doc/ja/source/tutorial/minsearch.rst | 14 +++++++------- doc/ja/source/tutorial/mpi.rst | 12 ++++++------ doc/ja/source/tutorial/pamc.rst | 10 +++++----- 10 files changed, 62 insertions(+), 62 deletions(-) diff --git a/doc/en/source/tutorial/bayes.rst b/doc/en/source/tutorial/bayes.rst index bcf80073..bc5c1370 100644 --- a/doc/en/source/tutorial/bayes.rst +++ b/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 diff --git a/doc/en/source/tutorial/exchange.rst b/doc/en/source/tutorial/exchange.rst index 6d1b13af..e6dce52c 100644 --- a/doc/en/source/tutorial/exchange.rst +++ b/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). diff --git a/doc/en/source/tutorial/minsearch.rst b/doc/en/source/tutorial/minsearch.rst index 3a668f21..3d20a633 100644 --- a/doc/en/source/tutorial/minsearch.rst +++ b/doc/en/source/tutorial/minsearch.rst @@ -22,7 +22,7 @@ In the main program, the Nelder-Mead method (using `scipy.optimize.fmin