Blocking scheme sampling

halmd/observables/dynamics/blocking_scheme.cpp

@@ -1,5 +1,7 @@
 /*
- * Copyright © 2011  Peter Colberg and Felix Höfling
+ * Copyright © 2011 Felix Höfling
+ * Copyright © 2015 Nicolas Höft
+ * Copyright © 2011 Peter Colberg
  *
  * This file is part of HALMD.
  *
@@ -150,6 +152,31 @@ void blocking_scheme::sample()
     on_append_sample_();
 }
 
+blocking_scheme::step_type blocking_scheme::next() const
+{
+    LOG_TRACE("compute next occurance of a sampling step");
+    step_type next_step;
+    step_type const step = clock_->step();
+
+    // TODO: is this sufficient?
+    next_step = step + separation_;
+
+    // iterate over all coarse-graining levels
+    for (unsigned int i = 0; i < interval_.size(); ++i) {
+        // calculate the next occuring sampling measured from step
+        step_type next;
+        if (origin_[i] < step) {
+            next = origin_[i] + ((step - 1 - origin_[i]) / interval_[i] + 1) * interval_[i];
+        }
+        else {
+            next = origin_[i];
+        }
+
+        next_step = min(next, next_step);
+    }
+    return next_step;
+}
+
 void blocking_scheme::finalise()
 {
     on_prepend_finalise_();
@@ -264,6 +291,7 @@ void blocking_scheme::luaopen(lua_State* L)
                     .def("on_append_sample", &blocking_scheme::on_append_sample)
                     .def("on_prepend_finalise", &blocking_scheme::on_prepend_finalise)
                     .def("on_append_finalise", &blocking_scheme::on_append_finalise)
+                    .def("next", &blocking_scheme::next)
             ]
         ]
     ];

halmd/observables/dynamics/blocking_scheme.hpp

@@ -119,6 +119,8 @@ class blocking_scheme
         return time_;
     }
 
+    step_type next() const;
+
     /** Lua bindings */
     static void luaopen(lua_State* L);
 

lua/halmd/observables/dynamics/blocking_scheme.lua.in

@@ -1,5 +1,6 @@
 --
 -- Copyright © 2011-2014 Felix Höfling
+-- Copyright © 2015      Nicolas Höft
 -- Copyright © 2011-2012 Peter Colberg
 --
 -- This file is part of HALMD.
@@ -123,13 +124,15 @@ local M = module(function(args)
         local conn = {}
         result.disconnect = utility.signal.disconnect(conn, "correlation function")
 
-        -- establish internal connections of the correlation function
-        -- e.g., particle:enable_aux() → sampler.on_prepare_force,
-        -- and append to our connection table
-        if tcf.connect then
-            conn_ = tcf:connect({every = every}) -- FIXME pass actual grid of sampling steps
-            for i,c in ipairs(conn_) do
-                table.insert(conn, c)
+        -- enable auxiliary variable calculation, if necessary for correlation function
+        if tcf.aux_enable then
+            local particles = utility.assert_type(tcf.aux_enable, "table")
+            for i,p in ipairs(particles) do
+                table.insert(conn, sampler:on_prepare(function()
+                    if self:next() == clock.step then
+                        p:aux_enable()
+                    end
+                end, 1, clock.step))
             end
         end
 

lua/halmd/observables/dynamics/correlation.lua.in

@@ -83,6 +83,7 @@ local blocking_scheme_adaptor = assert(libhalmd.observables.samples.blocking_sch
 -- :param args.location: default location within file
 -- :type args.location: string table
 -- :param string args.desc: module description
+-- :param table args.aux_enable: sequence of :class:`halmd.mdsim.particle` instances *(optional)*
 --
 -- The argument ``acquire`` is a callable or a table of up to 2 callables that
 -- yield the samples to be correlated.
@@ -95,6 +96,13 @@ local blocking_scheme_adaptor = assert(libhalmd.observables.samples.blocking_sch
 -- H5MD files, it obeys the structure {``"dynamics"``, particle group, name of
 -- correlation function}.
 --
+-- The parameter ``aux_enable`` is useful if ``acquire()`` depends on one of
+-- the auxiliary force variables, see :meth:`halmd.mdsim.particle.aux_enable`
+-- for details. In sampling steps of the correlation function, each ``particle``
+-- instance listed in ``aux_enable`` is notified to update the auxiliary
+-- variables before the sampling step. Thereby, redundant force calculations
+-- can be avoided.
+--
 -- .. method:: acquire()
 --
 --    Acquire sample(s).
@@ -113,6 +121,11 @@ local blocking_scheme_adaptor = assert(libhalmd.observables.samples.blocking_sch
 --
 --    Module description.
 --
+-- .. attribute:: aux_enable
+--
+--    Sequence of particle instances that require auxiliary variables
+--    during sampling.
+--
 -- .. class:: writer(args)
 --
 --    Construct file writer.
@@ -133,6 +146,7 @@ local M = module(function(args)
     local shape     = utility.assert_type(args.shape or {}, "table")
     local location  = utility.assert_type(utility.assert_kwarg(args, "location"), "table")
     local desc      = utility.assert_type(utility.assert_kwarg(args, "desc"), "string")
+    local aux_enable = utility.assert_type(args.aux_enable or {}, "table")
 
     -- ensure that acquire is a table
     if not (type(acquire) == "table") then
@@ -165,6 +179,10 @@ local M = module(function(args)
         return writer
     end end)
 
+    self.aux_enable = property(function(self)
+        return aux_enable
+    end)
+
     return self
 end)
 

lua/halmd/observables/dynamics/stress_tensor_autocorrelation.lua.in

@@ -1,5 +1,5 @@
 --
--- Copyright © 2013      Nicolas Höft
+-- Copyright © 2013-2015 Nicolas Höft
 -- Copyright © 2013-2014 Felix Höfling
 --
 -- This file is part of HALMD.
@@ -82,19 +82,6 @@ local sampler     = require("halmd.observables.sampler")
 --
 --    Module description.
 --
--- .. method:: connect(args)
---
---    :param table args: keyword arguments
---    :param args.every: sampling interval
---    :returns: sequence of signal connections
---
---    *Internal use only.* This function is called upon registration by
---    ``blocking_scheme:correlation()``.
---
---    Connect ``msv.group.particle:aux_enable()`` to the signal
---    ``on_prepend_force`` of :class:`halmd.observables.sampler` using the
---    interval ``every``.
---
 -- .. class:: writer(args)
 --
 --    Construct file writer.
@@ -136,17 +123,9 @@ local M = module(function(args)
       , location = {"dynamics", label, "stress_tensor_autocorrelation"}
         -- module description
       , desc = ("stress tensor autocorrelation of %s particles"):format(label)
+      , aux_enable = {msv.group.particle}
     }))
 
-    self.connect = function(self, args)
-        local every = utility.assert_kwarg(args, "every")
-
-        local conn = {
-            assert(sampler:on_prepare(function() msv.group.particle:aux_enable() end, every, clock.step))
-        }
-        return conn
-    end
-
     return self
 end)