Docs update

doc/dchf.rst

@@ -88,9 +88,9 @@ The minimal distance is kept constant at 1.4A.
 Case 3: Linear alkanes
 ======================
 
-The benchmark model is :math:`\mathrm{C_6 H_{14}}` split into 6 clusters by default.
+The benchmark model is :math:`\mathrm{C_{12} H_{26}}` split into ?? clusters by default.
 
-.. image:: plots/alkane-8-domains.svg
+.. image:: plots/alkane-12-domains.svg
 
 The density matrix
 ------------------

doc/plots/27-dchf-errors-locality-alkane.py

@@ -10,11 +10,17 @@
 
 tolerance = 1e-5
 
-draw_cluster_model("alkane-8", width=800, height=200)
+draw_cluster_model("alkane-12", width=800, height=200)
 
-dchf = load_pyscf_cluster_model("alkane-8", isolated_cluster=True)
+print "== 0 =="
+dchf = load_pyscf_cluster_model("alkane-12")
 dchf.__mol__.verbose = 4
 dchf.kernel()
+#
+# print "== 1 =="
+# del dchf.domains[1]
+# dchf.add_domain([1, 2, 3, 4, 5, 6, 7, 8, 9], core=[4, 5, 6], insert_at=1)
+# dchf.kernel()
 
 hf = scf.RHF(dchf.__mol__)
 hf.kernel()
@@ -31,7 +37,7 @@
         (dchf, 122, "DC-HF"),
 ):
     pyplot.subplot(subplot)
-    pyplot.imshow(abs(hf.dm if isinstance(hf, DCHF) else hf.make_rdm1()))
+    pyplot.imshow(abs(hf.dm if isinstance(hf, DCHF) else hf.make_rdm1()), vmin=0, vmax=2)
     pyplot.title(title)
     pyplot.colorbar()
 

doc/plots/fake.py

@@ -11,7 +11,7 @@ def p(x):
 
 
 class LogCalls(object):
-    def __init__(self, name, head="", line_start="", tail=""):
+    def __init__(self, name, head="", line_start="", tail="", proto=None):
         """A simple facility logging all method calls."""
         self.name = name
         if os.path.exists(name):
@@ -20,9 +20,12 @@ def __init__(self, name, head="", line_start="", tail=""):
         self.head = head
         self.line_start = line_start
         self.tail = tail
+        self.proto = proto
 
     def __getattr__(self, item):
         def __(*args, **kwargs):
+            if self.proto is not None:
+                getattr(self.proto, item)(*args, **kwargs)
             self.items.append(
                 dict(
                     __method_name__=item,
@@ -47,6 +50,7 @@ def __(*args, **kwargs):
 
 
 def pyplot(name=None):
+    from matplotlib import pyplot
     if name is None:
         name = inspect.stack()[1][1]
         if name[-3:] == ".py":
@@ -57,4 +61,5 @@ def pyplot(name=None):
         head="#/usr/bin/env python\n\"\"\"\nThis file was generated automatically.\n\"\"\"\nfrom matplotlib import pyplot",
         line_start="pyplot.",
         tail="\n",
+        proto=pyplot,
     )

doc/plots/models.json

@@ -14,15 +14,21 @@
       {"buffer": [2, 3, 11, 12, 6, 7, 15, 16, 17], "core": [4, 5, 13, 14]},
       {"buffer": [4, 5, 13, 14], "core": [6, 7, 15, 16, 17]}]
   },
-  "alkane-8": {
-    "pyscf-string": "H 4.42014622 4.16792406 3.37924476; C 5.29939098 3.54076487 3.37924476; H 5.29939098 2.91360568 4.25848952; H 5.29939098 2.91360568 2.50000000; C 6.45909854 4.36797623 3.37924476; H 6.45909854 4.99513542 4.25848952; H 6.45909854 4.99513542 2.50000000; C 7.61880609 3.54076487 3.37924476; H 7.61880609 2.91360568 4.25848952; H 7.61880609 2.91360568 2.50000000; C 8.77851365 4.36797623 3.37924476; H 8.77851365 4.99513542 4.25848952; H 8.77851365 4.99513542 2.50000000; C 9.93822121 3.54076487 3.37924476; H 9.93822121 2.91360568 4.25848952; H 9.93822121 2.91360568 2.50000000; C 11.09792876 4.36797623 3.37924476; H 11.09792876 4.99513542 4.25848952; H 11.09792876 4.99513542 2.50000000; H 11.97717352 3.74081704 3.37924476",
+  "alkane-12": {
+    "pyscf-string": "H 4.42014622 4.16792406 3.37924476; C 5.29939098 3.54076487 3.37924476; H 5.29939098 2.91360568 4.25848952; H 5.29939098 2.91360568 2.50000000; C 6.45909854 4.36797623 3.37924476; H 6.45909854 4.99513542 4.25848952; H 6.45909854 4.99513542 2.50000000; C 7.61880609 3.54076487 3.37924476; H 7.61880609 2.91360568 4.25848952; H 7.61880609 2.91360568 2.50000000; C 8.77851365 4.36797623 3.37924476; H 8.77851365 4.99513542 4.25848952; H 8.77851365 4.99513542 2.50000000; C 9.93822121 3.54076487 3.37924476; H 9.93822121 2.91360568 4.25848952; H 9.93822121 2.91360568 2.50000000; C 11.09792876 4.36797623 3.37924476; H 11.09792876 4.99513542 4.25848952; H 11.09792876 4.99513542 2.50000000; C 12.25763632 3.54076487 3.37924476; H 12.25763632 2.91360568 4.25848952; H 12.25763632 2.91360568 2.50000000; C 13.41734387 4.36797623 3.37924476; H 13.41734387 4.99513542 4.25848952; H 13.41734387 4.99513542 2.50000000; C 14.57705143 3.54076487 3.37924476; H 14.57705143 2.91360568 4.25848952; H 14.57705143 2.91360568 2.50000000; C 15.73675898 4.36797623 3.37924476; H 15.73675898 4.99513542 4.25848952; H 15.73675898 4.99513542 2.50000000; C 16.89646654 3.54076487 3.37924476; H 16.89646654 2.91360568 4.25848952; H 16.89646654 2.91360568 2.50000000; C 18.05617410 4.36797623 3.37924476; H 18.05617410 4.99513542 4.25848952; H 18.05617410 4.99513542 2.50000000; H 18.93541886 3.74081704 3.37924476",
     "domains": [
-      {"core": [0, 1, 2, 3], "buffer":[4, 5, 6, 7, 8, 9]},
-      {"core": [4, 5, 6], "buffer":[0, 1, 2, 3, 7, 8, 9, 10, 11, 12]},
-      {"core": [7, 8, 9], "buffer":[0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15]},
-      {"core": [10, 11, 12], "buffer":[4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18]},
-      {"core": [13, 14, 15], "buffer":[7, 8, 9, 10, 11, 12, 16, 17, 18, 19]},
-      {"core": [16, 17, 18, 19], "buffer":[10, 11, 12, 13, 14, 15]}
+      {"core": [0, 1, 2, 3], "buffer": []} ,
+      {"core": [4, 5, 6], "buffer": []} ,
+      {"core": [7, 8, 9], "buffer": []} ,
+      {"core": [10, 11, 12], "buffer": []} ,
+      {"core": [13, 14, 15], "buffer": []} ,
+      {"core": [16, 17, 18], "buffer": []} ,
+      {"core": [19, 20, 21], "buffer": []} ,
+      {"core": [22, 23, 24], "buffer": []} ,
+      {"core": [25, 26, 27], "buffer": []} ,
+      {"core": [28, 29, 30], "buffer": []} ,
+      {"core": [31, 32, 33], "buffer": []} ,
+      {"core": [34, 35, 36, 37], "buffer": []}
     ]
   },
   "graphite-cluster-6": {