Modified count_bonds.py to exclude bond counts with 0 bonds

Author: saforem2

worm_algorithm/block_configs.ipynb

@@ -14,7 +14,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-14T07:02:03.470104Z",
      "start_time": "2018-02-14T07:02:03.402771Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -57,7 +58,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-14T07:02:20.821016Z",
      "start_time": "2018-02-14T07:02:20.779909Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -82,7 +84,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-14T07:06:56.468428Z",
      "start_time": "2018-02-14T07:03:06.769141Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [
     {
@@ -314,7 +317,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-14T07:15:38.264660Z",
      "start_time": "2018-02-14T07:06:56.471148Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [
     {
@@ -540,7 +544,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-11T05:51:16.514653Z",
      "start_time": "2018-02-11T04:53:37.782988Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [
     {
@@ -755,7 +760,7 @@
      "end_time": "2018-02-14T08:53:44.026829Z",
      "start_time": "2018-02-14T07:18:52.813715Z"
     },
-    "scrolled": true
+    "collapsed": true
    },
    "outputs": [
     {
@@ -797,7 +802,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-11T04:16:04.973886Z",
      "start_time": "2018-02-11T04:16:04.207233Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -811,7 +817,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-11T04:16:30.116180Z",
      "start_time": "2018-02-11T04:16:30.076712Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [
     {
@@ -837,7 +844,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-11T04:18:18.992227Z",
      "start_time": "2018-02-11T04:18:18.961658Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -851,7 +859,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-11T04:18:22.609146Z",
      "start_time": "2018-02-11T04:18:22.567577Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [
     {
@@ -877,7 +886,7 @@
      "end_time": "2018-02-11T04:19:15.041598Z",
      "start_time": "2018-02-11T04:19:14.914851Z"
     },
-    "scrolled": false
+    "collapsed": true
    },
    "outputs": [
     {
@@ -1696,7 +1705,7 @@
      "end_time": "2018-02-11T04:18:42.076673Z",
      "start_time": "2018-02-11T04:18:41.947982Z"
     },
-    "scrolled": true
+    "collapsed": true
    },
    "outputs": [
     {
@@ -2514,7 +2523,8 @@
     "ExecuteTime": {
      "end_time": "2018-02-11T04:14:50.553525Z",
      "start_time": "2018-02-11T04:14:42.966791Z"
-    }
+    },
+    "collapsed": true
    },
    "outputs": [
     {
@@ -2547,7 +2557,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": []
   }
@@ -2569,7 +2581,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.6.5"
   },
   "latex_envs": {
    "LaTeX_envs_menu_present": true,

worm_algorithm/bonds.py

@@ -57,10 +57,10 @@ def __init__(self, L, run=False, num_steps=1E7, verbose=True,
         self._x_bonds = {}
         self._y_bonds = {}
         self._config_data = self.set_config_data()
-        self._blocked_config_data = self.block_configs(block_val)
         if write:
             self.write_config_data()
         if write_blocked:
+            self._blocked_config_data = self.block_configs(block_val)
             self.write_blocked_config_data()
 
     def _get_raw_bonds(self):

worm_algorithm/count_bonds.py

@@ -24,7 +24,7 @@ class CountBonds(object):
             Directory containing configuration data to be analyzed.
         _save_dir : (str)
             Directory where resulting bond_statistics data is to be written to.
-        _write : bool
+        _save : bool
             Whether or not to save the bond_statistics data.
         _verbose : bool
             Whether or not to display information as the analysis is being
@@ -111,6 +111,7 @@ def _count_bonds(self, data):
             np.sum([config[i] for i in bond_idxs]) for config in
             data.reshape(-1, w, w)
         ])
+        bc_arr = bc_arr[np.where(bc_arr != 0)]
         bc2_arr = bc_arr ** 2
         Nb_avg = np.mean(bc_arr)
         Nb2_avg = np.mean(bc2_arr)