From 1980fdd5d18b5da428ee2dea2c7ad88ae5250096 Mon Sep 17 00:00:00 2001
From: "P.M. Sutter" <sutter@iap.fr>
Date: Fri, 3 May 2013 14:44:40 -0400
Subject: [PATCH] added joggling of input particles

---
 c_tools/mock/generateMock.cpp                  | 18 ++++++++++++++++++
 c_tools/mock/generateMock.ggo                  |  1 +
 .../void_python_tools/backend/launchers.py     |  1 +
 3 files changed, 20 insertions(+)

diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp
index ff84ace..c47fd15 100644
--- a/c_tools/mock/generateMock.cpp
+++ b/c_tools/mock/generateMock.cpp
@@ -152,6 +152,21 @@ void metricTransform(SimuData *data, int axis, bool reshift, bool pecvel, double
 
 }
 
+// slightly perturb particle positions
+void joggleParticles(SimuData *data) {
+  gsl_rng *rng;
+  gsl_rng_set(rng, 31415926535);
+  for (uint32_t i = 0; i < data->NumPart; i++) {
+    data->Pos[0][i] += 1.e-3*gsl_rng_uniform(rng);
+    data->Pos[1][i] += 1.e-3*gsl_rng_uniform(rng); 
+    data->Pos[2][i] += 1.e-3*gsl_rng_uniform(rng);
+    data->Pos[0][i] -= 1.e-3*gsl_rng_uniform(rng);
+    data->Pos[1][i] -= 1.e-3*gsl_rng_uniform(rng); 
+    data->Pos[2][i] -= 1.e-3*gsl_rng_uniform(rng);
+  }
+  }
+} // end joggleParticles
+
 void generateOutput(SimuData *data, int axis, 
 		    const std::string& fname)
 {
@@ -723,6 +738,9 @@ int main(int argc, char **argv)
       delete[] efac;
     }
 
+  if (args_info.jogglePartices_give)
+    joggleParticles(simuOut)   
+ 
   saveBox(simuOut, args_info.outputParameter_arg, args_info);
   generateOutput(simuOut, args_info.axis_arg, 
                  args_info.output_arg);
diff --git a/c_tools/mock/generateMock.ggo b/c_tools/mock/generateMock.ggo
index fe441e6..5041272 100644
--- a/c_tools/mock/generateMock.ggo
+++ b/c_tools/mock/generateMock.ggo
@@ -41,3 +41,4 @@ option "subsample_seed" - "Seed for random number generation to select the subsa
 option "resubsample" - "Resubsampling factor compared to the subsampled simulation" double optional 
 option "resubsample_seed" - "Seed for resubsampling from a subsampled simulation" int optional default="20132011"
 
+option "joggleParticles"	- "Slightly joggle the input particle positions" flag off
diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py
index 7dda879..d16ca39 100644
--- a/python_tools/void_python_tools/backend/launchers.py
+++ b/python_tools/void_python_tools/backend/launchers.py
@@ -189,6 +189,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
       %s
       %s
       %s
+      joggleParticles
       """ % (dataFileLine, outputFile,
              outputFile+".par",
              includePecVelString,