added usage in en

Author: yomichi

docs/sphinx/en/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c3c689d1f40c918c842861556f4cf854
+config: 754b678b8b4ca4523c90f554812f8dc1
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/sphinx/en/build/html/_sources/how_to_use/basic_usage.rst.txt

@@ -43,11 +43,93 @@ The following is an example of an input file selecting QE as a solver.
 Execution
 ========================
 
-The number of processes specified here must be the same as the number of replicas.
+The number of processes specified here must be greater than or equal to the number of replicas.
 
-(Various matters derived from MPI_Comm_spawn (the actual process to be allocated, mpiexec options, etc. need to be described somewhere)
 
 ::
 
  $ mpiexec -np 2 abics input.toml
 
+This creates a directory named with the replica number under the current directory, and each replica runs the solver in it.
+
+
+Tips for the number of MPI processes
+========================================
+abICS uses the MPI library function ``MPI_Comm_spawn`` to run the solver.
+This function executes another program on new MPI processes.
+
+For example, consider that you have a parallel machine with 4 CPU cores per node
+and want to run two replicas and to invoke solvers on 4 CPU cores.
+If invoked as ``mpiexec -np2 abics input.toml``, the replica control processes A and B are started on the first two cores of node 0,
+each starting a new four-parallel solver a and b.
+Then, solver a fills the remaining two cores in node 0 and the first two cores in node 1,
+and solver b is placed on the remaining two cores in node 1 and the first two cores in node 2.
+This causes inter-node communication within the solver and reduces performance.
+
+By taking more of the initial process, you can align the processes and prevent unnecessary node stripping.
+In this example, ``mpiexec -np 4 abics input.toml`` will allow the replica control processes A and B to fill all the cores of the node 0, while solvers a and b fill nodes 1 and 2, respectively.
+
+
+Comments on MPI implementation
+====================================
+In the ``MPI_Comm_spawn`` function, a MPI implementation can use the information "how many process can be started in total" by ``MPI_UNIVERSE_SIZE``.
+In this seciton, we will comment on some MPI implementations including how to set ``MPI_UNIVERSE_SIZE``.
+
+OpenMPI
+~~~~~~~~~~~~~
+``MPI_UNIVERSE_SIZE`` is automatically set to the number of the CPU cores available.
+If you want more processes, you should pass the ``--oversubscribe`` option to the ``mpiexec`` command.
+
+When one of the spawned process returns a nonzero return code, all the OpenMPI processes will abort.
+The ``--mca orte_abort_on_non_zero_status 0`` option allows you to ignore the return code.
+Quantum ESPRESSO, for example, may return a nonzero value due to a floating point exception even if the calculation is successfully completed.
+
+MPICH / Intel MPI
+~~~~~~~~~~~~~~~~~~~~~
+The ``-usize <num>`` option set ``MPI_UNIVERSE_SIZE``.
+Indeed, MPICH and Intel MPI seem not to use this value in ``MPI_Comm_spawn``.
+
+HPE (SGI) MPT
+~~~~~~~~~~~~~~~~~~~
+The ``-up <num>`` option set ``MPI_UNIVERSE_SIZE``.
+This must be set before the ``-np <num>`` option.
+
+Others
+~~~~~~~~~~
+On large supercomputers, the vendor may provide a dedicated MPI execution script along with the job scheduler.
+In this case, refer to the manuals.
+On the ISSP supercomputer systems, Sekirei and Enaga, for example, ``mpijob -spawn`` sets ``MPI_UNIVERSE_SIZE`` properly.
+
+
+The output of abics
+---------------------
+The calculation results are output below each replica directory.
+
+``structure.XXX.vasp``
+=========================
+The atomic position for each step in the POSCAR file format of VASP is saved.
+``XXX`` in the filename means the index of the step.
+
+``minE.vasp``
+====================
+The atomic position minimizing the total energy in the POSCAR file format of VASP is saved.
+
+``obs.dat``
+===================
+The temperature and the total energy for each step in units of eV is saved.
+
+``obs_save.npy``
+==================
+The total energy for each step in units of eV in the Numpy binary format is saved.
+Users can load it as ``darray`` by using ``numpy.load('obs_save.npy')``.
+
+``kT_hist.npy``
+==================
+The temperature for each step in units of eV in the Numpy binary format is saved.
+Users can load it as ``darray`` by using ``numpy.load('kT_hist.npy')``.
+
+``Trank_hist.npy``
+==================
+The rank (index) of the temperature for each step in the Numpy binary format is saved.
+Users can load it as ``darray`` by using ``numpy.load('Trank_hist.npy')``.
+

docs/sphinx/en/build/html/_sources/install/install.rst.txt

@@ -3,9 +3,9 @@
 Download
 ~~~~~~~~~~~~~~~~~~~~~~
 
-The source codes of abICS can be obtained from `GitHub page <https://github.com/issp-center-dev/pymc-dev>`_ .
+The source codes of abICS can be obtained from `GitHub page <https://github.com/issp-center-dev/abICS>`_ .
 
-``$ git clone https://github.com/issp-center-dev/pymc-dev``
+``$ git clone https://github.com/issp-center-dev/abICS``
 
 Prerequisites
 ~~~~~~~~~~~~~~~~~~~~~~

docs/sphinx/en/build/html/_static/alabaster.css

@@ -166,6 +166,19 @@ div.sphinxsidebar hr {
     width: 50%;
 }
 
+div.sphinxsidebar .badge {
+    border-bottom: none;
+}
+
+div.sphinxsidebar .badge:hover {
+    border-bottom: none;
+}
+
+/* To address an issue with donation coming after search */
+div.sphinxsidebar h3.donation {
+    margin-top: 10px;
+}
+
 /* -- body styles ----------------------------------------------------------- */
 
 a {
@@ -314,7 +327,7 @@ p.admonition-title:after {
 }
 
 pre, tt, code {
-    font-family: 'Consolas', 'Menlo', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+    font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
     font-size: 0.9em;
 }
 

docs/sphinx/en/build/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -81,10 +81,26 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
 div.sphinxsidebar #searchbox input[type="text"] {
-    width: 170px;
+    float: left;
+    width: 80%;
+    padding: 0.25em;
+    box-sizing: border-box;
 }
 
+div.sphinxsidebar #searchbox input[type="submit"] {
+    float: left;
+    width: 20%;
+    border-left: none;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+
 img {
     border: 0;
     max-width: 100%;
@@ -199,6 +215,11 @@ table.modindextable td {
 
 /* -- general body styles --------------------------------------------------- */
 
+div.body {
+    min-width: 450px;
+    max-width: 800px;
+}
+
 div.body p, div.body dd, div.body li, div.body blockquote {
     -moz-hyphens: auto;
     -ms-hyphens: auto;
@@ -210,6 +231,16 @@ a.headerlink {
     visibility: hidden;
 }
 
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -332,6 +363,11 @@ table.docutils {
     border-collapse: collapse;
 }
 
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
 table caption span.caption-number {
     font-style: italic;
 }
@@ -365,6 +401,16 @@ table.citation td {
     border-bottom: none;
 }
 
+th > p:first-child,
+td > p:first-child {
+    margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+    margin-bottom: 0px;
+}
+
 /* -- figures --------------------------------------------------------------- */
 
 div.figure {
@@ -405,6 +451,13 @@ table.field-list td, table.field-list th {
     hyphens: manual;
 }
 
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+    vertical-align: top;
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {
@@ -427,11 +480,57 @@ ol.upperroman {
     list-style: upper-roman;
 }
 
+li > p:first-child {
+    margin-top: 0px;
+}
+
+li > p:last-child {
+    margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: flex;
+    flex-wrap: wrap;
+}
+
+dl.field-list > dt {
+    flex-basis: 20%;
+    font-weight: bold;
+    word-break: break-word;
+}
+
+dl.field-list > dt:after {
+    content: ":";
+}
+
+dl.field-list > dd {
+    flex-basis: 70%;
+    padding-left: 1em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
 dl {
     margin-bottom: 15px;
 }
 
-dd p {
+dd > p:first-child {
     margin-top: 0px;
 }
 
@@ -445,10 +544,14 @@ dd {
     margin-left: 30px;
 }
 
-dt:target, .highlighted {
+dt:target, span.highlighted {
     background-color: #fbe54e;
 }
 
+rect.highlighted {
+    fill: #fbe54e;
+}
+
 dl.glossary dt {
     font-weight: bold;
     font-size: 1.1em;
@@ -500,6 +603,12 @@ dl.glossary dt {
     font-style: oblique;
 }
 
+.classifier:before {
+    font-style: normal;
+    margin: 0.5em;
+    content: ":";
+}
+
 abbr, acronym {
     border-bottom: dotted 1px;
     cursor: help;