[Avida-SVN] r2686 - in branches/uml-merge: documentation source/main
dk at myxo.css.msu.edu
dk at myxo.css.msu.edu
Wed Jun 25 07:08:01 PDT 2008
Author: dk
Date: 2008-06-25 10:08:00 -0400 (Wed, 25 Jun 2008)
New Revision: 2686
Modified:
branches/uml-merge/documentation/index.html
branches/uml-merge/documentation/svn.html
branches/uml-merge/source/main/cPopulation.cc
branches/uml-merge/source/main/cResourceCount.cc
branches/uml-merge/source/main/cSpatialCountElem.h
branches/uml-merge/source/main/cSpatialResCount.cc
Log:
Merged 2671:2684 development->uml-merge.
Modified: branches/uml-merge/documentation/index.html
===================================================================
--- branches/uml-merge/documentation/index.html 2008-06-25 14:04:41 UTC (rev 2685)
+++ branches/uml-merge/documentation/index.html 2008-06-25 14:08:00 UTC (rev 2686)
@@ -5,6 +5,7 @@
</head>
<body>
+
<div align="center">
<table border="0">
<tr>
Modified: branches/uml-merge/documentation/svn.html
===================================================================
--- branches/uml-merge/documentation/svn.html 2008-06-25 14:04:41 UTC (rev 2685)
+++ branches/uml-merge/documentation/svn.html 2008-06-25 14:08:00 UTC (rev 2686)
@@ -43,14 +43,11 @@
<p>
To download the Avida project, issue the 'checkout' command with the path
to the Avida repository. The following two command lines show how this
-command should look and provide the repository paths. The first line is
-the preferred path. The second can be used in instances where outbound
-firewalls have blocked access to non-standard web ports.
+command should look and provide the repository paths.
</p>
<pre>
-svn checkout http://myxo.css.msu.edu:7632/avida/trunk
-svn checkout http://myxo.css.msu.edu:443/avida/trunk
+svn checkout https://avida.devosoft.org/svn/development
</pre>
@@ -113,4 +110,4 @@
<p><a href="index.html">Return to the Index</a></p>
</body>
-</html>
\ No newline at end of file
+</html>
Modified: branches/uml-merge/source/main/cPopulation.cc
===================================================================
--- branches/uml-merge/source/main/cPopulation.cc 2008-06-25 14:04:41 UTC (rev 2685)
+++ branches/uml-merge/source/main/cPopulation.cc 2008-06-25 14:08:00 UTC (rev 2686)
@@ -1153,6 +1153,12 @@
}
}
+ //re-inject demes with count of 1 back into self
+ for(int i = 0; i < (int)deme_counts.size(); i++) {
+ if(deme_counts[i] == 1)
+ ReplaceDeme(deme_array[i], deme_array[i]);
+ }
+
// Now, while we can find both a source deme (one with a count greater than 1)
// and a target deme (one with a count of 0), replace the target with the source.
while(true) {
Modified: branches/uml-merge/source/main/cResourceCount.cc
===================================================================
--- branches/uml-merge/source/main/cResourceCount.cc 2008-06-25 14:04:41 UTC (rev 2685)
+++ branches/uml-merge/source/main/cResourceCount.cc 2008-06-25 14:08:00 UTC (rev 2686)
@@ -493,7 +493,25 @@
}
void cResourceCount::ReinitializeResources(double additional_resource){
+ cSpatialResCount src;
+ double c_curr_amount;
+ double c_initial_amount;
+ double c_new_amount;
+
for(int i = 0; i < resource_name.GetSize(); i++) {
- Set(i, resource_initial[i]+additional_resource); //will cause problem if more than one resource is used.
- }
-}
+ Set(i, resource_initial[i]+additional_resource); //will cause problem if more than one resource is used. -- why? each resource is stored separately (BDC)
+
+ // Additionally, set any initial values given by the CELL command
+ src = GetSpatialResource(i);
+ for(int j = 0; j < src.GetSize(); j++) {
+ c_initial_amount = src.Element(j).GetInitial();
+ if(c_initial_amount > 0) {
+ c_curr_amount = spatial_resource_count[i].GetAmount(j);
+ c_new_amount = c_curr_amount + c_initial_amount + additional_resource;
+ spatial_resource_count[i].SetCellAmount(j, c_new_amount);
+ }
+ }
+
+ } //End going through the resources
+
+} //End ReinitializeResources()
Modified: branches/uml-merge/source/main/cSpatialCountElem.h
===================================================================
--- branches/uml-merge/source/main/cSpatialCountElem.h 2008-06-25 14:04:41 UTC (rev 2685)
+++ branches/uml-merge/source/main/cSpatialCountElem.h 2008-06-25 14:08:00 UTC (rev 2686)
@@ -33,7 +33,7 @@
class cSpatialCountElem
{
private:
- mutable double amount, delta;
+ mutable double amount, delta, initial;
tArray<int> elempt, xdist, ydist;
tArray<double> dist;
@@ -52,6 +52,8 @@
double GetPtrDist(int innum) { return dist[innum]; }
friend void FlowMatter(cSpatialCountElem&, cSpatialCountElem&, double, double, double, double,
int, int, double);
+ void SetInitial(double init) { initial = init; }
+ double GetInitial() { return initial; }
};
Modified: branches/uml-merge/source/main/cSpatialResCount.cc
===================================================================
--- branches/uml-merge/source/main/cSpatialResCount.cc 2008-06-25 14:04:41 UTC (rev 2685)
+++ branches/uml-merge/source/main/cSpatialResCount.cc 2008-06-25 14:08:00 UTC (rev 2686)
@@ -226,6 +226,7 @@
if (cell_id >= 0 && cell_id <= grid.GetSize()) {
Rate((*cell_list_ptr)[i].GetId(), (*cell_list_ptr)[i].GetInitial());
State((*cell_list_ptr)[i].GetId());
+ Element(cell_id).SetInitial((*cell_list_ptr)[i].GetInitial());
}
}
}
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