Merge pull request #10 from MDIL-SNU/python3

Python3

README

@@ -77,24 +77,21 @@ Brief description of each file:
 #               Installation                 #
 ##############################################
 
-AMP2 is written in Python 2.7. Currently, the
-package is not compatible with lower or higher
-version than 2.7. AMP2 is utilizes Python modules
-in the following with link to each site.
+AMP2 supprots Python 2.7 and 3. Currently, the
+package is not compatible with lower version
+than 2.7. AMP2 is utilizes Python modules in 
+the following with link to each site.
   - numpy [https://www.numpy.org]
   - scipy [https://www.scipy.org]
   - spglib [https://atztogo.github.io/spglib]
+  - PyYAML [https://pypi.org/project/PyYAML]
 These modules should be pre-installed. In addition,
 AMP2 needs gnuplot to draw various figures.
 
 ##############################################
 #                Basic setup                 #
 ##############################################
 
-As we mentioned, AMP2 was written in Python 2.7. 
-Thus, to use AMP2, you should set to execute Python
-2.7 from 'python' command.
-----------------------------------------------
 AMP2 uses YAML style configuration file. All 
 setting parameters used in AMP2 can be controlled
 in 'config.yaml'. Before using AMP2, proper pathes
@@ -128,8 +125,12 @@ python [src_path]/main.py [path for configuration file] [path for nodefile] [the
 
 - [src_path] is the path for directory of source codes for AMP2.
 - [path for configuration file] is the path for configuration file (config.yaml).
-- [path for nodefile] is used to record the information of computing nodes.
+- [path for nodefile] is used to record the information of computing nodes such as
+  PBS_nodefile in Portable Batch System {PBS} and HOSTNAME in Sun Grid Engine (SGE).
+  In the PBS system, we recommand to use the command, "echo $PBS_nodefile > nodefile".
+  Also, users can save an arbitrary text by writing in the nodefile.
 - [the number of cores] is the number of cores to be used in parallel computing.
+
 For the convenience, we provide the shell script file (run.sh) as following.
 
 ================= run.sh ===================

docs/Input/Advanced_configuration.rst

@@ -103,4 +103,58 @@ config_def.yaml:
         - hole
         - electron
       temperature_for_fermi: 300            # The temperature to estimate the Fermi distribution
-      fermi_for_cutoff: 0.99                # Boundary condition for valid Fermi distribution (1-f)
+      fermi_for_cutoff: 0.99                # Boundary condition for valid Fermi distribution (1-f)
+
+To get more accurate band gap
+-----------------------------
+
+We suggest two approaches to get more accurate band gap.
+
+- Band calculation with hybrid functional
+
+  In the basic version, the band calculation is performed using PBE scheme.
+  However, users can add the tags below to use hybrid functional for structure
+  optimization and band calculation.
+  ::
+    relaxation:
+      potential_type:
+        - HSE
+    band_calculation:
+      potential_type:
+        - HSE
+
+- Using HSE@PBE scheme with hybrid structure
+
+  Second approach is still using HSE@PBE method but the optimized structure is 
+  calculated using hybrid functional. Since the band calculation with hybrid functional
+  is too expensive, the k-points corresponding to the VBM and CBM are determined by using
+  GGA method. For this calculation, users can use the commands below. Here, if potential_type
+  in hybrid_oneshot is the main category, the method tags (HSE and GGA) are child subcategory 
+  not parent subcategory. Please be careful.
+  ::
+    relaxation:
+      potential_type:
+        - GGA
+        - HSE
+    hybrid_oneshot:
+      potential_type:
+        - - HSE
+          - GGA
+
+Organic crystal
+---------------
+Organic crystals usually have lower Young's modulus than inorganic materials.
+Thus, the error in the structural parameters can be substantial and they require
+high precision for calculation. The tags below can control the precision of calculation.
+::
+  cif2vasp:
+    INCAR:
+      EDIFF: 1e-08
+
+  convergence_test:
+    enconv: 0.001
+    prconv: 1
+
+  relaxation:
+    pressure: 1
+    force: 0.002

docs/Input/Configuration.rst

@@ -414,3 +414,16 @@ The details are explained in the paper.
               carrier_type:
                 - hole
                 - electron
+
+    - temperature_for_fermi:
+        It controls the temperature to estimate the hole or electron distribution 
+        based on the Fermi-Dirac function.
+
+        Usage:
+        ::
+            effective_mass:
+              temperature_for_fermi: [real]
+        Default:
+        ::
+            effective_mass:
+              temperature_for_fermi: 300

docs/Installation/Installation.rst

@@ -62,9 +62,9 @@ You can execute AMP\ :sup:`2`\  using Python command as following.
 - [src_path] is the path for directory of source codes for AMP\ :sup:`2`\.
 - [path for configuration file] is the path for configuration file (config.yaml).
 - [path for nodefile] is used to record the information of computing nodes such as PBS_nodefile in 
-Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use
-the command, "echo $PBS_nodefile > nodefile". Also, users can save an arbitrary text
-by writing in the nodefile.
+  Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use
+  the command, "echo $PBS_nodefile > nodefile". Also, users can save an arbitrary text
+  by writing in the nodefile.
 - [the number of cores] is the number of cores to be used in parallel computing.
 
 For the convenience, we provide the shell script file (run.sh) as following.
@@ -88,4 +88,4 @@ Then, you can execute AMP\ :sup:`2`\  using shell script as following.
     sh run.sh
 
 The shell script file can be easily integrated with job scheduler program such 
-as PBS.
+as PBS.

docs/_build/html/Input/Advanced_configuration.html

@@ -91,7 +91,11 @@
 <li class="toctree-l1 current"><a class="reference internal" href="Input.html">Input</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="Input_files.html">Input files</a></li>
 <li class="toctree-l2"><a class="reference internal" href="Configuration.html">Configuration</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Advanced configuration</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Advanced configuration</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#to-get-more-accurate-band-gap">To get more accurate band gap</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#organic-crystal">Organic crystal</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../Output/Output.html">Output</a></li>
@@ -267,6 +271,62 @@ <h1>Advanced configuration<a class="headerlink" href="#advanced-configuration" t
   <span class="n">fermi_for_cutoff</span><span class="p">:</span> <span class="mf">0.99</span>                <span class="c1"># Boundary condition for valid Fermi distribution (1-f)</span>
 </pre></div>
 </div>
+<div class="section" id="to-get-more-accurate-band-gap">
+<h2>To get more accurate band gap<a class="headerlink" href="#to-get-more-accurate-band-gap" title="Permalink to this headline">¶</a></h2>
+<p>We suggest two approaches to get more accurate band gap.</p>
+<ul>
+<li><p>Band calculation with hybrid functional</p>
+<p>In the basic version, the band calculation is performed using PBE scheme.
+However, users can add the tags below to use hybrid functional for structure
+optimization and band calculation.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">relaxation</span><span class="p">:</span>
+  <span class="n">potential_type</span><span class="p">:</span>
+    <span class="o">-</span> <span class="n">HSE</span>
+<span class="n">band_calculation</span><span class="p">:</span>
+  <span class="n">potential_type</span><span class="p">:</span>
+    <span class="o">-</span> <span class="n">HSE</span>
+</pre></div>
+</div>
+</li>
+<li><p>Using <a class="reference external" href="mailto:HSE&#37;&#52;&#48;PBE">HSE<span>&#64;</span>PBE</a> scheme with hybrid structure</p>
+<p>Second approach is still using <a class="reference external" href="mailto:HSE&#37;&#52;&#48;PBE">HSE<span>&#64;</span>PBE</a> method but the optimized structure is
+calculated using hybrid functional. Since the band calculation with hybrid functional
+is too expensive, the k-points corresponding to the VBM and CBM are determined by using
+GGA method. For this calculation, users can use the commands below. Here, if potential_type
+in hybrid_oneshot is the main category, the method tags (HSE and GGA) are child subcategory
+not parent subcategory. Please be careful.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">relaxation</span><span class="p">:</span>
+  <span class="n">potential_type</span><span class="p">:</span>
+    <span class="o">-</span> <span class="n">GGA</span>
+    <span class="o">-</span> <span class="n">HSE</span>
+<span class="n">hybrid_oneshot</span><span class="p">:</span>
+  <span class="n">potential_type</span><span class="p">:</span>
+    <span class="o">-</span> <span class="o">-</span> <span class="n">HSE</span>
+      <span class="o">-</span> <span class="n">GGA</span>
+</pre></div>
+</div>
+</li>
+</ul>
+</div>
+<div class="section" id="organic-crystal">
+<h2>Organic crystal<a class="headerlink" href="#organic-crystal" title="Permalink to this headline">¶</a></h2>
+<p>Organic crystals usually have lower Young’s modulus than inorganic materials.
+Thus, the error in the structural parameters can be substantial and they require
+high precision for calculation. The tags below can control the precision of calculation.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cif2vasp</span><span class="p">:</span>
+  <span class="n">INCAR</span><span class="p">:</span>
+    <span class="n">EDIFF</span><span class="p">:</span> <span class="mf">1e-08</span>
+
+<span class="n">convergence_test</span><span class="p">:</span>
+  <span class="n">enconv</span><span class="p">:</span> <span class="mf">0.001</span>
+  <span class="n">prconv</span><span class="p">:</span> <span class="mi">1</span>
+
+<span class="n">relaxation</span><span class="p">:</span>
+  <span class="n">pressure</span><span class="p">:</span> <span class="mi">1</span>
+  <span class="n">force</span><span class="p">:</span> <span class="mf">0.002</span>
+</pre></div>
+</div>
+</div>
 </div>
 
 

docs/_build/html/Input/Configuration.html

@@ -682,6 +682,22 @@ <h2>Effective_mass<a class="headerlink" href="#effective-mass" title="Permalink
 </dd>
 </dl>
 </li>
+<li><dl>
+<dt>temperature_for_fermi:</dt><dd><p>It controls the temperature to estimate the hole or electron distribution
+based on the Fermi-Dirac function.</p>
+<p>Usage:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">effective_mass</span><span class="p">:</span>
+  <span class="n">temperature_for_fermi</span><span class="p">:</span> <span class="p">[</span><span class="n">real</span><span class="p">]</span>
+</pre></div>
+</div>
+<p>Default:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">effective_mass</span><span class="p">:</span>
+  <span class="n">temperature_for_fermi</span><span class="p">:</span> <span class="mi">300</span>
+</pre></div>
+</div>
+</dd>
+</dl>
+</li>
 </ul>
 </div></blockquote>
 </div>

docs/_build/html/Input/Input.html

@@ -179,7 +179,11 @@ <h1>Input<a class="headerlink" href="#input" title="Permalink to this headline">
 <li class="toctree-l2"><a class="reference internal" href="Configuration.html#effective-mass">Effective_mass</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="Advanced_configuration.html">Advanced configuration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Advanced_configuration.html">Advanced configuration</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Advanced_configuration.html#to-get-more-accurate-band-gap">To get more accurate band gap</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Advanced_configuration.html#organic-crystal">Organic crystal</a></li>
+</ul>
+</li>
 </ul>
 </div>
 </div>

docs/_build/html/Installation/Installation.html

@@ -36,7 +36,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Overview" href="../Overview/Overview.html" />
-    <link rel="prev" title="Welcome to AMP2’s documentation!" href="../index.html" /> 
+    <link rel="prev" title="AMP2 Manual" href="../index.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -230,12 +230,12 @@ <h2>Execution AMP<sup>2</sup><a class="headerlink" href="#execution-amp2" title=
 <ul class="simple">
 <li><p>[src_path] is the path for directory of source codes for AMP<sup>2</sup>.</p></li>
 <li><p>[path for configuration file] is the path for configuration file (config.yaml).</p></li>
-<li><p>[path for nodefile] is used to record the information of computing nodes such as PBS_nodefile in</p></li>
-</ul>
-<p>Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use
+<li><p>[path for nodefile] is used to record the information of computing nodes such as PBS_nodefile in
+Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use
 the command, “echo $PBS_nodefile &gt; nodefile”. Also, users can save an arbitrary text
-by writing in the nodefile.
-- [the number of cores] is the number of cores to be used in parallel computing.</p>
+by writing in the nodefile.</p></li>
+<li><p>[the number of cores] is the number of cores to be used in parallel computing.</p></li>
+</ul>
 <p>For the convenience, we provide the shell script file (run.sh) as following.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>echo &#39;node information&#39; &gt; nodefile
 NPROC=16       # The number of cores for parallel computing
@@ -272,7 +272,7 @@ <h2>Execution AMP<sup>2</sup><a class="headerlink" href="#execution-amp2" title=
         <a href="../Overview/Overview.html" class="btn btn-neutral float-right" title="Overview" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="../index.html" class="btn btn-neutral float-left" title="Welcome to AMP2’s documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="../index.html" class="btn btn-neutral float-left" title="AMP2 Manual" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

docs/_build/html/_sources/Input/Advanced_configuration.rst.txt

@@ -103,4 +103,58 @@ config_def.yaml:
         - hole
         - electron
       temperature_for_fermi: 300            # The temperature to estimate the Fermi distribution
-      fermi_for_cutoff: 0.99                # Boundary condition for valid Fermi distribution (1-f)
+      fermi_for_cutoff: 0.99                # Boundary condition for valid Fermi distribution (1-f)
+
+To get more accurate band gap
+-----------------------------
+
+We suggest two approaches to get more accurate band gap.
+
+- Band calculation with hybrid functional
+
+  In the basic version, the band calculation is performed using PBE scheme.
+  However, users can add the tags below to use hybrid functional for structure
+  optimization and band calculation.
+  ::
+    relaxation:
+      potential_type:
+        - HSE
+    band_calculation:
+      potential_type:
+        - HSE
+
+- Using HSE@PBE scheme with hybrid structure
+
+  Second approach is still using HSE@PBE method but the optimized structure is 
+  calculated using hybrid functional. Since the band calculation with hybrid functional
+  is too expensive, the k-points corresponding to the VBM and CBM are determined by using
+  GGA method. For this calculation, users can use the commands below. Here, if potential_type
+  in hybrid_oneshot is the main category, the method tags (HSE and GGA) are child subcategory 
+  not parent subcategory. Please be careful.
+  ::
+    relaxation:
+      potential_type:
+        - GGA
+        - HSE
+    hybrid_oneshot:
+      potential_type:
+        - - HSE
+          - GGA
+
+Organic crystal
+---------------
+Organic crystals usually have lower Young's modulus than inorganic materials.
+Thus, the error in the structural parameters can be substantial and they require
+high precision for calculation. The tags below can control the precision of calculation.
+::
+  cif2vasp:
+    INCAR:
+      EDIFF: 1e-08
+
+  convergence_test:
+    enconv: 0.001
+    prconv: 1
+
+  relaxation:
+    pressure: 1
+    force: 0.002

docs/_build/html/_sources/Input/Configuration.rst.txt

@@ -414,3 +414,16 @@ The details are explained in the paper.
               carrier_type:
                 - hole
                 - electron
+
+    - temperature_for_fermi:
+        It controls the temperature to estimate the hole or electron distribution 
+        based on the Fermi-Dirac function.
+
+        Usage:
+        ::
+            effective_mass:
+              temperature_for_fermi: [real]
+        Default:
+        ::
+            effective_mass:
+              temperature_for_fermi: 300

docs/_build/html/_sources/Installation/Installation.rst.txt

@@ -62,9 +62,9 @@ You can execute AMP\ :sup:`2`\  using Python command as following.
 - [src_path] is the path for directory of source codes for AMP\ :sup:`2`\.
 - [path for configuration file] is the path for configuration file (config.yaml).
 - [path for nodefile] is used to record the information of computing nodes such as PBS_nodefile in 
-Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use
-the command, "echo $PBS_nodefile > nodefile". Also, users can save an arbitrary text
-by writing in the nodefile.
+  Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use
+  the command, "echo $PBS_nodefile > nodefile". Also, users can save an arbitrary text
+  by writing in the nodefile.
 - [the number of cores] is the number of cores to be used in parallel computing.
 
 For the convenience, we provide the shell script file (run.sh) as following.
@@ -88,4 +88,4 @@ Then, you can execute AMP\ :sup:`2`\  using shell script as following.
     sh run.sh
 
 The shell script file can be easily integrated with job scheduler program such 
-as PBS.
+as PBS.