diff --git a/Atlas_Figure.html b/Atlas_Figure.html index 9bd8103..567e8c1 100644 --- a/Atlas_Figure.html +++ b/Atlas_Figure.html @@ -330,7 +330,7 @@

Make Atlas
{"steps": 1000, "n_particles": 2, "time_step": 0.005, "seed": 435423, "anderson_nu": 100, "langevin_gamma": 10, "bussi_taut": 0.5, "thermostat_seed": 54344, "rcut": 10, "skin": 0.6000000000000001, "temperature": 0.01, "pressure": null, "box_update_period": 0, "start_temperature": 0.5, "thermostat": "baoab", "force_type": "lj", "final_positions": "crystal-6-2/group-6.dat", "cell_log_file": "crystal-6-2/cell_log_file.dat", "print_period": 10000.0, "cell": [6.32465, 0.0, 0.0, 6.32465], "lj_epsilon": 1, "lj_sigma": 1.0, "n_images": 2, "start_positions": "crystal-6-2/group-6.dat", "group": "crystal-6-2/group-6.json"}
-Info: You are running version c07a of symd
+Info: You are running version fd57 of symd
 Assuming you'll pass parameters via stdin. Waiting...
 Warning: assuming default value for position_log_period = 0
 Warning: assuming default value for velocity_log_period = 0
@@ -366,7 +366,7 @@ 
Make Atlas
-
[<matplotlib.lines.Line2D at 0x7f9ad0c3bfd0>]
+
[<matplotlib.lines.Line2D at 0x7f2a3af092e0>]
 

 

 _images/Atlas_Figure_7_1.png
@@ -379,7 +379,7 @@ 
Make Atlas
-
[<matplotlib.lines.Line2D at 0x7f9ad14b2fa0>]
+
[<matplotlib.lines.Line2D at 0x7f2a3b03d130>]
 

 

 _images/Atlas_Figure_8_1.png
@@ -457,7 +457,7 @@ 
Plot Figure
-
('atlas2d.pkl.gz', <http.client.HTTPMessage at 0x7f9ad1464640>)
+
('atlas2d.pkl.gz', <http.client.HTTPMessage at 0x7f2a3afe1ac0>)
 

 

 

@@ -518,7 +518,7 @@ 
Plot Figure
-
_images/Atlas_Figure_14_1.png
+
_images/Atlas_Figure_14_1.png
 

 

 

@@ -531,7 +531,7 @@ 
Plot Figure
-
/tmp/ipykernel_2351/3025209989.py:3: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
+
/tmp/ipykernel_2301/3025209989.py:3: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
   fig, ax = plt.subplots(figsize=figsize)
 

 

@@ -626,7 +626,7 @@ 
Plot Figure
-
_images/Atlas_Figure_16_1.png
+
_images/Atlas_Figure_16_1.png
 _images/Atlas_Figure_16_2.png
 _images/Atlas_Figure_16_3.png
 _images/Atlas_Figure_16_4.png
@@ -654,17 +654,6 @@ 
Plot Figure
-
---------------------------------------------------------------------------
-ModuleNotFoundError                       Traceback (most recent call last)
-Input In [15], in <cell line: 1>()
-----> 1 from cairosvg import svg2png
-      3 svg2png(bytestring=svg, write_to="atlas_raster.png", dpi=300)
-
-ModuleNotFoundError: No module named 'cairosvg'
-

-

-

 

 
 

@@ -675,6 +664,11 @@ 
TOC<
+
+
['p1', 'p2', 'pm', 'pg', 'cm', 'pmm', 'pmg', 'pgg', 'cmm', 'p4', 'p4m', 'p4g', 'p3', 'p3m1', 'p31m', 'p6', 'p6m']
+
+
+
@@ -725,6 +719,13 @@

TOC<

+
+
128 6 3150 21 150
+3150
+
+
+_images/Atlas_Figure_20_1.png +
diff --git a/Custom_Group.html b/Custom_Group.html index 06b7b77..2c75e50 100644 --- a/Custom_Group.html +++ b/Custom_Group.html @@ -200,7 +200,7 @@

Run< 
{"steps": 1000000, "n_particles": 256, "time_step": 0.005, "seed": 435423, "anderson_nu": 100, "langevin_gamma": 0.5, "bussi_taut": 0.5, "thermostat_seed": 54344, "rcut": 10, "skin": 0.6000000000000001, "temperature": 0.1, "pressure": 0.25, "box_update_period": 10, "start_temperature": 0.1, "thermostat": "baoab", "force_type": "lj", "final_positions": "quasi/final_positions.dat", "cell_log_file": "quasi/cell_log_file.dat", "print_period": 10000.0, "cell": [38.0257, 0.0, 0.0, 37.0197], "lj_epsilon": 1, "lj_sigma": 1, "images": [0, 0], "wyckoffs": [{"group": "quasi/group-custom-00.json", "n_particles": 1}], "start_positions": "quasi/final_positions.dat", "group": "quasi/group-custom.json", "position_log_period": 1000, "positions_log_file": "quasi/positions.xyz"}
-Info: You are running version c07a of symd
+Info: You are running version fd57 of symd
 Assuming you'll pass parameters via stdin. Waiting...
 Warning: assuming default value for velocity_log_period = 0
 Warning: assuming default value for force_log_period = 0
@@ -256,7 +256,7 @@ 
Run<
-
[<matplotlib.lines.Line2D at 0x7f5c20245220>]
+
[<matplotlib.lines.Line2D at 0x7fa8d4a02370>]
 

 

 _images/Custom_Group_7_1.png
diff --git a/Energy_Figure.html b/Energy_Figure.html
index 3434ade..d862abc 100644
--- a/Energy_Figure.html
+++ b/Energy_Figure.html
@@ -193,7 +193,7 @@ 
Figure 1 from Paper
-
<matplotlib.legend.Legend at 0x7f7512930f70>
+
<matplotlib.legend.Legend at 0x7fd219393e50>
 

 

 _images/Energy_Figure_5_1.png
@@ -226,7 +226,7 @@ 
All Sims
 
{"steps": 1000, "n_particles": 4, "time_step": 0.005, "seed": 435423, "anderson_nu": 100, "langevin_gamma": 10, "bussi_taut": 0.5, "thermostat_seed": 54344, "rcut": 10, "skin": 0.6000000000000001, "temperature": 0.01, "pressure": null, "box_update_period": 0, "start_temperature": 0.5, "thermostat": "baoab", "force_type": "lj", "final_positions": "sim2d/group-3.dat", "cell_log_file": "sim2d/cell_log_file.dat", "print_period": 300.0, "cell": [2.71442, 0.0, 0.0, 0.0, 2.71442, 0.0, 0.0, 0.0, 2.71442], "lj_epsilon": 1, "lj_sigma": 1.0, "n_images": 2, "start_positions": "sim2d/group-3.dat", "group": "sim2d/group-3.json"}
-Info: You are running version c07a of symd
+Info: You are running version fd57 of symd
 Assuming you'll pass parameters via stdin. Waiting...
 Warning: assuming default value for position_log_period = 0
 Warning: assuming default value for velocity_log_period = 0
@@ -257,7 +257,7 @@ 
All Sims
{"steps": 1000, "n_particles": 4, "time_step": 0.005, "seed": 435423, "anderson_nu": 100, "langevin_gamma": 10, "bussi_taut": 0.5, "thermostat_seed": 54344, "rcut": 10, "skin": 0.6000000000000001, "temperature": 0.01, "pressure": null, "box_update_period": 0, "start_temperature": 0.5, "thermostat": "baoab", "force_type": "lj", "final_positions": "sim2d/group-6.dat", "cell_log_file": "sim2d/cell_log_file.dat", "print_period": 300.0, "cell": [2.71442, 0.0, 0.0, 0.0, 2.71442, 0.0, 0.0, 0.0, 2.71442], "lj_epsilon": 1, "lj_sigma": 1.0, "n_images": 2, "start_positions": "sim2d/group-6.dat", "group": "sim2d/group-6.json"}
-Info: You are running version c07a of symd
+Info: You are running version fd57 of symd
 Assuming you'll pass parameters via stdin. Waiting...
 Warning: assuming default value for position_log_period = 0
 Warning: assuming default value for velocity_log_period = 0
@@ -287,7 +287,7 @@ 
All Sims
{"steps": 1000, "n_particles": 4, "time_step": 0.005, "seed": 435423, "anderson_nu": 100, "langevin_gamma": 10, "bussi_taut": 0.5, "thermostat_seed": 54344, "rcut": 10, "skin": 0.6000000000000001, "temperature": 0.01, "pressure": null, "box_update_period": 0, "start_temperature": 0.5, "thermostat": "baoab", "force_type": "lj", "final_positions": "sim2d/group-10.dat", "cell_log_file": "sim2d/cell_log_file.dat", "print_period": 300.0, "cell": [3.41995, 0.0, 0.0, 0.0, 3.41995, 0.0, 0.0, 0.0, 3.41995], "lj_epsilon": 1, "lj_sigma": 1.0, "n_images": 2, "start_positions": "sim2d/group-10.dat", "group": "sim2d/group-10.json"}
-Info: You are running version c07a of symd
+Info: You are running version fd57 of symd
 Assuming you'll pass parameters via stdin. Waiting...
 Warning: assuming default value for position_log_period = 0
 Warning: assuming default value for velocity_log_period = 0
@@ -317,7 +317,7 @@ 
All Sims
{"steps": 1000, "n_particles": 4, "time_step": 0.005, "seed": 435423, "anderson_nu": 100, "langevin_gamma": 10, "bussi_taut": 0.5, "thermostat_seed": 54344, "rcut": 10, "skin": 0.6000000000000001, "temperature": 0.01, "pressure": null, "box_update_period": 0, "start_temperature": 0.5, "thermostat": "baoab", "force_type": "lj", "final_positions": "sim2d/group-11.dat", "cell_log_file": "sim2d/cell_log_file.dat", "print_period": 300.0, "cell": [3.41995, 0.0, 0.0, 0.0, 3.41995, 0.0, 0.0, 0.0, 3.41995], "lj_epsilon": 1, "lj_sigma": 1.0, "n_images": 2, "start_positions": "sim2d/group-11.dat", "group": "sim2d/group-11.json"}
-Info: You are running version c07a of symd
+Info: You are running version fd57 of symd
 Assuming you'll pass parameters via stdin. Waiting...
 Warning: assuming default value for position_log_period = 0
 Warning: assuming default value for velocity_log_period = 0
diff --git a/Tutorial.html b/Tutorial.html
index 55bec81..580fcf8 100644
--- a/Tutorial.html
+++ b/Tutorial.html
@@ -328,8 +328,8 @@ 
Bravais Lattice
 
This lattice is Square
-[[2.60993268 0.        ]
- [0.         2.60993268]]
+[[2.13484562 0.        ]
+ [0.         2.13484562]]
 

 

 

@@ -351,7 +351,7 @@ 
Bravais Lattice
-
The volume of my cell is 6.811748614407135
+
The volume of my cell is 4.5575658136274395
 If I have 8 particles in asymmetric unit, there will be 64 in the unit cell
 

 

diff --git a/_images/Atlas_Figure_20_1.png b/_images/Atlas_Figure_20_1.png
new file mode 100644
index 0000000..91aab09
Binary files /dev/null and b/_images/Atlas_Figure_20_1.png differ
diff --git a/_images/Tutorial_10_0.png b/_images/Tutorial_10_0.png
index af518f4..8ff26af 100644
Binary files a/_images/Tutorial_10_0.png and b/_images/Tutorial_10_0.png differ
diff --git a/_images/Tutorial_13_0.png b/_images/Tutorial_13_0.png
index 6cecc25..d5f4d5d 100644
Binary files a/_images/Tutorial_13_0.png and b/_images/Tutorial_13_0.png differ
diff --git a/_images/Tutorial_16_0.png b/_images/Tutorial_16_0.png
index 92effc9..9172700 100644
Binary files a/_images/Tutorial_16_0.png and b/_images/Tutorial_16_0.png differ
diff --git a/_images/Tutorial_20_0.png b/_images/Tutorial_20_0.png
index b408a3b..b8ca042 100644
Binary files a/_images/Tutorial_20_0.png and b/_images/Tutorial_20_0.png differ
diff --git a/_images/Tutorial_8_0.png b/_images/Tutorial_8_0.png
index a02a8dd..44464e6 100644
Binary files a/_images/Tutorial_8_0.png and b/_images/Tutorial_8_0.png differ
diff --git a/_sources/changelog.rst.txt b/_sources/changelog.rst.txt
index 2e7606c..15bae74 100644
--- a/_sources/changelog.rst.txt
+++ b/_sources/changelog.rst.txt
@@ -1,6 +1,11 @@
 Change Log
 ==========
 
+v1.1.2 (2022-11-20)
+--------------------
+* Fixed incorrect cubic, tetragonal, and hexagonal projectors in 3D
+
+
 v1.1.0 (2022-6-26)
 -------------------
 * Added names of space groups
diff --git a/changelog.html b/changelog.html
index 5cd47de..9b1ad3a 100644
--- a/changelog.html
+++ b/changelog.html
@@ -47,6 +47,7 @@
               
    
 
  • Getting Started
    • 
 
  • Change Log
      
+
    • v1.1.2 (2022-11-20)
      • 
 
    • v1.1.0 (2022-6-26)
      • 
 
    • v1.0.2 (2022-4-4)
      • 
 
    • v1.0.1 (2022-4-3)
      • 
@@ -86,6 +87,12 @@
              
   
      
 
      Change Log
      
+
      
+
      v1.1.2 (2022-11-20)
      
+
        
+
      • Fixed incorrect cubic, tetragonal, and hexagonal projectors in 3D
        • 
+
      
+
      
 
      
 
      v1.1.0 (2022-6-26)
      
 
        
diff --git a/objects.inv b/objects.inv
index 3428c37..cec5166 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/reports/Atlas_Figure.log b/reports/Atlas_Figure.log
deleted file mode 100644
index ddc41cc..0000000
--- a/reports/Atlas_Figure.log
+++ /dev/null
@@ -1,33 +0,0 @@
-Traceback (most recent call last):
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
-    executenb(
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/nbclient/client.py", line 1204, in execute
-    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/nbclient/util.py", line 84, in wrapped
-    return just_run(coro(*args, **kwargs))
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/nbclient/util.py", line 62, in just_run
-    return loop.run_until_complete(coro)
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
-    return future.result()
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/nbclient/client.py", line 663, in async_execute
-    await self.async_execute_cell(
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/nbclient/client.py", line 965, in async_execute_cell
-    await self._check_raise_for_error(cell, cell_index, exec_reply)
-  File "/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/nbclient/client.py", line 862, in _check_raise_for_error
-    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
-nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
-------------------
-from cairosvg import svg2png
-
-svg2png(bytestring=svg, write_to="atlas_raster.png", dpi=300)
-------------------
-
----------------------------------------------------------------------------
-ModuleNotFoundError                       Traceback (most recent call last)
-Input In [15], in ()
-----> 1 from cairosvg import svg2png
-      3 svg2png(bytestring=svg, write_to="atlas_raster.png", dpi=300)
-
-ModuleNotFoundError: No module named 'cairosvg'
-ModuleNotFoundError: No module named 'cairosvg'
-
diff --git a/searchindex.js b/searchindex.js
index 7aa527b..c8a830b 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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+++ b/toc.html
@@ -86,6 +86,7 @@ 
        symd
 
      
 
 
    • Change Log