Merge pull request #18 from MDIL-SNU/python3

Python3

README

@@ -86,7 +86,8 @@ the following with link to each site.
   - 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.
+AMP2 needs gnuplot supporting 'pngcairo' and 
+'pdfcairo' to draw various figures.
 
 ##############################################
 #                Basic setup                 #

docs/Input/Configuration.rst

@@ -273,7 +273,7 @@ npar and kpar tags are used to enhance the efficiency of parallel computing calc
               npar: 2
 
     - kpar: 
-        kpar tag determines the number of kpoints that are treated in parallel. It is same to NPAR tag in VASP.
+        kpar tag determines the number of kpoints that are treated in parallel. It is same to KPAR tag in VASP.
 
         Usage:
         ::

docs/Installation/Installation.rst

@@ -16,8 +16,8 @@ System requirements
     - spglib [https://atztogo.github.io/spglib]
     - PyYAML [https://pypi.org/project/PyYAML]
 
-    These modules should be pre-installed. In addition, AMP\ :sup:`2`\  needs gnuplot to draw
-    various figures.
+    These modules should be pre-installed. In addition, AMP\ :sup:`2`\  needs gnuplot
+    supporting 'pngcairo' and 'pdfcairo' to draw various figures.
 
 
 Installation

docs/_build/html/Examples/Examples.html

@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input/Advanced_configuration.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input/Configuration.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 
@@ -511,7 +511,7 @@ <h2>Vasp_parallel<a class="headerlink" href="#vasp-parallel" title="Permalink to
 </dl>
 </li>
 <li><dl>
-<dt>kpar:</dt><dd><p>kpar tag determines the number of kpoints that are treated in parallel. It is same to NPAR tag in VASP.</p>
+<dt>kpar:</dt><dd><p>kpar tag determines the number of kpoints that are treated in parallel. It is same to KPAR tag in VASP.</p>
 <p>Usage:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">vasp_parallel</span><span class="p">:</span>
   <span class="n">kpar</span><span class="p">:</span> <span class="p">[</span><span class="n">integer</span><span class="p">]</span>

docs/_build/html/Input/Input.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input/Input_files.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Band_calculation.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Calculation.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Convergence_test.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Density_of_states.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Dielectric.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Directory.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Effective_mass.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Hybrid_oneshot.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Magnetic_ordering.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Program.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Relaxation.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/Vasp_parallel.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/cif2vasp.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/genetic_algorithm.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/potential.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Configuration/small_gap_correction.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Input_and_Output/Input_and_Output.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Installation/Installation.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 
@@ -183,8 +183,8 @@ <h3>System requirements<a class="headerlink" href="#system-requirements" title="
 <li><p>spglib [<a class="reference external" href="https://atztogo.github.io/spglib">https://atztogo.github.io/spglib</a>]</p></li>
 <li><p>PyYAML [<a class="reference external" href="https://pypi.org/project/PyYAML">https://pypi.org/project/PyYAML</a>]</p></li>
 </ul>
-<p>These modules should be pre-installed. In addition, AMP<sup>2</sup> needs gnuplot to draw
-various figures.</p>
+<p>These modules should be pre-installed. In addition, AMP<sup>2</sup> needs gnuplot
+supporting ‘pngcairo’ and ‘pdfcairo’ to draw various figures.</p>
 </div></blockquote>
 </div>
 <div class="section" id="installation">

docs/_build/html/Output/Output.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 

docs/_build/html/Overview/Overview.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.9.5
+                0.9.6
               </div>
 
 
@@ -194,14 +194,14 @@ <h2>Preparing input files<a class="headerlink" href="#preparing-input-files" tit
 <p>Structure file (VASP structure file format):</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Primitive Cell
    1.000000000
-      0.0    2.714895    2.714895
-      2.714895    0.0    2.714895
+      0.0         2.714895    2.714895
+      2.714895    0.0         2.714895
       2.714895    2.714895    0.0
     Si
     2
 Selective dynamics
 Direct
-    0.5    0.5    0.5  T  T  T ! Si1
+    0.5     0.5     0.5   T  T  T ! Si1
     0.75    0.75    0.75  T  T  T ! Si1
 </pre></div>
 </div>
@@ -227,8 +227,8 @@ <h2>Outputs<a class="headerlink" href="#outputs" title="Permalink to this headli
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>relaxed poscar
 1.000000000
     2.53085784423    1.46119145764    4.60391533726
-    -2.53085784423    1.46119145764    4.60391533726
-    0.0    -2.9223829153    4.60391533726
+   -2.53085784423    1.46119145764    4.60391533726
+    0.0             -2.9223829153     4.60391533726
     Cr    O
     4    6
 Selective dynamics
@@ -237,12 +237,12 @@ <h2>Outputs<a class="headerlink" href="#outputs" title="Permalink to this headli
     0.848055231569    0.848055231569    0.848055231569  T  T  T ! Cr1_up
     0.151944768431    0.151944768431    0.151944768431  T  T  T ! Cr1_down
     0.651944768431    0.651944768431    0.651944768431  T  T  T ! Cr1_down
-    0.553903778143    0.946096221857    0.25  T  T  T ! O1
-    0.946096221857    0.25    0.553903778143  T  T  T ! O1
-    0.25    0.553903778143    0.946096221857  T  T  T ! O1
-    0.0539037781426    0.75    0.446096221857  T  T  T ! O1
-    0.75    0.446096221857    0.0539037781426  T  T  T ! O1
-    0.446096221857    0.0539037781426    0.75  T  T  T ! O1
+    0.553903778143    0.946096221857    0.25            T  T  T ! O1
+    0.946096221857    0.25              0.553903778143  T  T  T ! O1
+    0.25              0.553903778143    0.946096221857  T  T  T ! O1
+    0.0539037781426   0.75              0.446096221857  T  T  T ! O1
+    0.75              0.446096221857    0.0539037781426 T  T  T ! O1
+    0.446096221857    0.0539037781426   0.75            T  T  T ! O1
 </pre></div>
 </div>
 <p>Band_gap_GGA.log:</p>
@@ -335,7 +335,8 @@ <h2>List of source codes<a class="headerlink" href="#list-of-source-codes" title
 </dl>
 </li>
 <li><dl class="simple">
-<dt>rerun_for_metal.py:</dt><dd><p>This is a code to restart the all calculations without the on-site Uterm if the material was found to be metallic and Uwas applied.</p>
+<dt>rerun_for_metal.py:</dt><dd><p>This is a code to restart the all calculations without the on-site <em>U</em>
+term if the material was found to be metallic and <em>U</em> was applied.</p>
 </dd>
 </dl>
 </li>
@@ -361,7 +362,7 @@ <h2>List of source codes<a class="headerlink" href="#list-of-source-codes" title
 </dl>
 </li>
 <li><dl class="simple">
-<dt>z_subr.py:</dt><dd><p>This is a package of modules for ’mk_supercell.py’.</p>
+<dt>module_subr.py:</dt><dd><p>This is a package of modules for ‘mk_supercell.py’.</p>
 </dd>
 </dl>
 </li>
@@ -370,7 +371,11 @@ <h2>List of source codes<a class="headerlink" href="#list-of-source-codes" title
 </dd>
 </dl>
 </li>
-<li><p>module_converge.py: This is a package of modules for convergence test.</p></li>
+<li><dl class="simple">
+<dt>module_converge.py:</dt><dd><p>This is a package of modules for convergence test.</p>
+</dd>
+</dl>
+</li>
 <li><dl class="simple">
 <dt>module_relax.py:</dt><dd><p>This is a package of modules for structure optimization.</p>
 </dd>
@@ -430,12 +435,12 @@ <h2>List of source codes<a class="headerlink" href="#list-of-source-codes" title
 <p>Additionally, there are files for predefined variables.</p>
 <ul class="simple">
 <li><dl class="simple">
-<dt>INCAR0:</dt><dd><p>This is for default configuration for ’INCAR’.</p>
+<dt>INCAR0:</dt><dd><p>This is for default configuration for ‘INCAR’.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt>U_table.yaml:</dt><dd><p>This is for default Uparameters.</p>
+<dt>U_table.yaml:</dt><dd><p>This is for default <em>U</em> parameters.</p>
 </dd>
 </dl>
 </li>
@@ -445,7 +450,7 @@ <h2>List of source codes<a class="headerlink" href="#list-of-source-codes" title
 </dl>
 </li>
 <li><dl class="simple">
-<dt>config_def.yaml:</dt><dd><p>This is default configuration for ’config.yaml’.</p>
+<dt>config_def.yaml:</dt><dd><p>This is default configuration for ‘config.yaml’.</p>
 </dd>
 </dl>
 </li>

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

@@ -273,7 +273,7 @@ npar and kpar tags are used to enhance the efficiency of parallel computing calc
               npar: 2
 
     - kpar: 
-        kpar tag determines the number of kpoints that are treated in parallel. It is same to NPAR tag in VASP.
+        kpar tag determines the number of kpoints that are treated in parallel. It is same to KPAR tag in VASP.
 
         Usage:
         ::

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

@@ -16,8 +16,8 @@ System requirements
     - spglib [https://atztogo.github.io/spglib]
     - PyYAML [https://pypi.org/project/PyYAML]
 
-    These modules should be pre-installed. In addition, AMP\ :sup:`2`\  needs gnuplot to draw
-    various figures.
+    These modules should be pre-installed. In addition, AMP\ :sup:`2`\  needs gnuplot
+    supporting 'pngcairo' and 'pdfcairo' to draw various figures.
 
 
 Installation