Add usage explanations; fix crystal position

Author: peter17

README.rst

@@ -19,6 +19,12 @@ Several types of inclusions can be defined:
 
 Crystalpy supports unit tests with nosetests.
 
+Usage
+=====
+
+* Define the geometry of your crystal in mesh.py
+* Run `python mesh.py`
+
 Versions
 ========
 
@@ -31,3 +37,4 @@ Versions
 * v. 2.4: Add unit tests; fix periodicity conditions
 * v. 2.5: Add support for physical points; fix 2D crystal generation
 * v. 2.6: Add support for physical lines; fix 2D image generation
+* v. 2.7: Add usage explanations; fix crystal position

generator.py

@@ -3,7 +3,7 @@
 
 from __future__ import division
 import pysvg
-from pysvg.builders import *
+from pysvg.builders import StyleBuilder
 from pysvg.core import *
 from pysvg.structure import *
 from pysvg.shape import *
@@ -754,14 +754,19 @@ def __init__(self,
                 el_size_value = Value(el_size_name, type.el_size)
                 type.el_size = el_size_value
 
+        dim_crystal_x = (nb_x - 1) * space_x
+        dim_crystal_y = (nb_y - 1) * space_y
+        crystal_base_x = pos_x - dim_crystal_x / 2
+        crystal_base_y = pos_y - dim_crystal_y / 2
+
         for i in range(nb_x):
             for j in range(nb_y):
                 if crystal_shape == 'hexa' and j % 2 == 1:
-                    x = pos_x + i * space_x + space_x / 2
-                    y = pos_y + j * space_y
+                    x = crystal_base_x + i * space_x + space_x / 2
+                    y = crystal_base_y + j * space_y
                 else:
-                    x = pos_x + i * space_x
-                    y = pos_y + j * space_y
+                    x = crystal_base_x + i * space_x
+                    y = crystal_base_y + j * space_y
                 type_id = 0 if inclusion_map is None else inclusion_map[j][i]
                 type = inclusion_types[type_id]
                 if type is not None:

mesh.py

@@ -54,8 +54,8 @@
      'nb_y': 2,
      'space_x': 250,
      'space_y': 250,
-     'pos_x': -125,
-     'pos_y': -125,
+     'pos_x': 0,
+     'pos_y': 0,
      'crystal_shape': 'square',
      'el_size_bulk': 25,
      'bulk_tag': 'mat1',

tests/test_image_2d.py

@@ -33,8 +33,8 @@ def test_square_mesh_2d(self):
              'nb_y': 2,
              'space_x': 250,
              'space_y': 250,
-             'pos_x': -125,
-             'pos_y': -125,
+             'pos_x': 0,
+             'pos_y': 0,
              'crystal_shape': 'square',
              'el_size_bulk': 25,
              'bulk_tag': 'mat1',
@@ -47,7 +47,7 @@ def test_square_mesh_2d(self):
 <rect style="stroke-width:1.5; " height="100" width="150" stroke="black" y="-175.0" x="-200.0" fill="grey"  />
 <rect style="stroke-width:1.5; " height="100" width="150" stroke="black" y="75.0" x="-200.0" fill="grey"  />
 <rect style="stroke-width:1.5; " height="100" width="150" stroke="black" y="-175.0" x="50.0" fill="grey"  />
-<ellipse style="stroke-width:1.5; " rx="75.0" ry="50.0" stroke="black" cy="125" cx="125" fill="lightgrey"  />
+<ellipse style="stroke-width:1.5; " rx="75.0" ry="50.0" stroke="black" cy="125.0" cx="125.0" fill="lightgrey"  />
 </svg>
 """
         self.image_equal_string(simple_2d, expected)

tests/test_mesh_2d.py

@@ -39,8 +39,8 @@ def test_square_mesh_2d(self):
              'nb_y': 2,
              'space_x': 250,
              'space_y': 250,
-             'pos_x': -125,
-             'pos_y': -125,
+             'pos_x': 0,
+             'pos_y': 0,
              'crystal_shape': 'square',
              'el_size_bulk': 25,
              'bulk_tag': 'mat1',
@@ -72,11 +72,11 @@ def test_square_mesh_2d(self):
 Point(17) = {50.0, -175.0, 0, size_1};
 Point(18) = {200.0, -75.0, 0, size_1};
 Point(19) = {200.0, -175.0, 0, size_1};
-Point(20) = {125, 125, 0, size_2};
-Point(21) = {50.0, 125, 0, size_2};
-Point(22) = {200.0, 125, 0, size_2};
-Point(23) = {125, 175.0, 0, size_2};
-Point(24) = {125, 75.0, 0, size_2};
+Point(20) = {125.0, 125.0, 0, size_2};
+Point(21) = {50.0, 125.0, 0, size_2};
+Point(22) = {200.0, 125.0, 0, size_2};
+Point(23) = {125.0, 175.0, 0, size_2};
+Point(24) = {125.0, 75.0, 0, size_2};
 Point(25) = {-250.0, 250.0, 0, size_bulk};
 Point(26) = {-250.0, -250.0, 0, size_bulk};
 Point(27) = {250.0, 250.0, 0, size_bulk};

tests/test_mesh_3d.py

@@ -38,8 +38,8 @@ def test_square_mesh_3d(self):
              'nb_y': 2,
              'space_x': 250,
              'space_y': 250,
-             'pos_x': -125,
-             'pos_y': -125,
+             'pos_x': 0,
+             'pos_y': 0,
              'crystal_shape': 'square',
              'el_size_bulk': 25,
              'bulk_tag': 'mat1',
@@ -81,16 +81,16 @@ def test_square_mesh_3d(self):
 Point(27) = {50.0, -175.0, -150, size_1};
 Point(28) = {200.0, -75.0, -150, size_1};
 Point(29) = {200.0, -175.0, -150, size_1};
-Point(30) = {125, 125, 0, size_2};
-Point(31) = {50.0, 125, 0, size_2};
-Point(32) = {200.0, 125, 0, size_2};
-Point(33) = {125, 175.0, 0, size_2};
-Point(34) = {125, 75.0, 0, size_2};
-Point(35) = {125, 125, 300, size_2};
-Point(36) = {50.0, 125, 300, size_2};
-Point(37) = {200.0, 125, 300, size_2};
-Point(38) = {125, 175.0, 300, size_2};
-Point(39) = {125, 75.0, 300, size_2};
+Point(30) = {125.0, 125.0, 0, size_2};
+Point(31) = {50.0, 125.0, 0, size_2};
+Point(32) = {200.0, 125.0, 0, size_2};
+Point(33) = {125.0, 175.0, 0, size_2};
+Point(34) = {125.0, 75.0, 0, size_2};
+Point(35) = {125.0, 125.0, 300, size_2};
+Point(36) = {50.0, 125.0, 300, size_2};
+Point(37) = {200.0, 125.0, 300, size_2};
+Point(38) = {125.0, 175.0, 300, size_2};
+Point(39) = {125.0, 75.0, 300, size_2};
 Point(40) = {-250.0, 250.0, 0, size_bulk};
 Point(41) = {-250.0, -250.0, 0, size_bulk};
 Point(42) = {250.0, 250.0, 0, size_bulk};