From f778d6cf03c85ccb6976931ac3178fb37cc80931 Mon Sep 17 00:00:00 2001
From: DeshanPerera <desh.02236@gmail.com>
Date: Wed, 2 Oct 2024 01:57:15 -0600
Subject: [PATCH] usermanual_update

---
 .vscode/launch.json                           |   4 ++--
 Test_main                                     | Bin 9488128 -> 9488128 bytes
 .../all_Profiles/profile_1.json               |   8 ++-----
 .../individual_Profiles/node_Master.json      |   2 +-
 parameters_Apollo/parameters_MASTER.json      |  21 +++++++++---------
 .../sequence_Profiles/sequence_Master.json    |  19 ++++++----------
 simulator_Master.cu                           |   2 +-
 7 files changed, 24 insertions(+), 32 deletions(-)

diff --git a/.vscode/launch.json b/.vscode/launch.json
index 74d9d74..ec12ff3 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -10,8 +10,8 @@
             "request": "launch",
             "program": "${fileDirname}/${fileBasenameNoExtension}",
             "args": [
-                "-h",
-                "/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/parameters_MASTER.json"
+                "-sim",
+                "/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Cancer_test/parameters_MASTER.json"
             ],
             "stopAtEntry": false,
             "cwd": "${fileDirname}",
diff --git a/Test_main b/Test_main
index 05d5a9489ee7359fff49d1e62b53b01b0c74ee75..5109c8da3843f4f65f8090b41edc0d994916d149 100644
GIT binary patch
delta 3936
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diff --git a/parameters_Apollo/individual_Profiles/all_Profiles/profile_1.json b/parameters_Apollo/individual_Profiles/all_Profiles/profile_1.json
index 822de62..69465e0 100644
--- a/parameters_Apollo/individual_Profiles/all_Profiles/profile_1.json
+++ b/parameters_Apollo/individual_Profiles/all_Profiles/profile_1.json
@@ -55,11 +55,9 @@
       "Cell limit Binomial trials":100000,
       "Cell limit Binomial probability":"0.10",
 
-      "Viral distribution type":"Gamma",
+      "Viral distribution type":"Binomial",
       "Viral distribution Binomial trials":10,
       "Viral distribution Binomial probability":"0.5",
-      "Viral distribution Gamma shape":"3",
-      "Viral distribution Gamma scale":"3.33",
 
       "Replication phases":{
 
@@ -73,15 +71,13 @@
     },
 
     "Tissue 3":{
-      "Cell limit":"NO",
+      "Cell limit":"Yes",
       "Cell limit Binomial trials":100000,
       "Cell limit Binomial probability":"0.10",
 
       "Viral distribution type":"Binomial",
       "Viral distribution Binomial trials":10,
       "Viral distribution Binomial probability":"0.5",
-      "Viral distribution Gamma shape":"3",
-      "Viral distribution Gamma scale":"3.33",
 
       "Replication phases":{
 
diff --git a/parameters_Apollo/individual_Profiles/node_Master.json b/parameters_Apollo/individual_Profiles/node_Master.json
index 33fc009..008f65d 100644
--- a/parameters_Apollo/individual_Profiles/node_Master.json
+++ b/parameters_Apollo/individual_Profiles/node_Master.json
@@ -40,7 +40,7 @@
   "Infected to Recovered":"No",
 
   "Number of node profiles":3,
-  "Location of node profiles":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/individual_Profiles/all_Profiles",
+  "Location of node profiles":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/individual_Profiles/all_Profiles",
 
   "Tissue profiles":{
 
diff --git a/parameters_Apollo/parameters_MASTER.json b/parameters_Apollo/parameters_MASTER.json
index a6c9d81..7c960fd 100644
--- a/parameters_Apollo/parameters_MASTER.json
+++ b/parameters_Apollo/parameters_MASTER.json
@@ -4,9 +4,9 @@
   "CUDA Device IDs":"0",
 
   # Hardware configuration parameters
-  "CPU cores":5,
+  "CPU cores":10,
   "GPU max units":1000,
-  "Process cell rate":10,
+  "Process cell rate":100,
   "Multi read":"YES",
 
   # Output and Intermediate folder locations.
@@ -16,30 +16,31 @@
   # The maximum number of sequences that can be stored in an intermeiate file
   "Intermediate Sequences per file":1000,
 
+  "Seed":"x",
+
   # Indicates the start date for the simulation
-  "Start date":"2024-01-10",
-  # Indicates the mode of infecting patient zero's within host environment. FIXED or RANDOM
+  "Start date":"2024-01-01",
   "First infection":"Random",
 
   # Indicate whether the user wants to run the simulation for a specified period of time
   "Stop after generations":"Yes",
   # Generations or Date can be used to stop the simulation as well
-  "Mode to stop":"Generations",
+  "Mode to stop":"Date",
   "Number of generations":3,
-  "End date":"2024-01-12",
+  "End date":"2024-04-01",
 
   # Network profile parameter file location
-  "Network profile":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/network_Profiles/network_test.json",
+  "Network profile":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/network_Profiles/network_test.json",
 
   # Node profile parameter file location
-  "Nodes master profile":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/individual_Profiles/node_Master.json",
+  "Nodes master profile":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/individual_Profiles/node_Master.json",
 
   # Sequence profiles parameter file location
-  "Sequence master profile":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/sequence_Profiles/sequence_Master.json",
+  "Sequence master profile":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/sequence_Profiles/sequence_Master.json",
 
   # Folder management controls
   # Compresses folders to a TAR.GZ or reduces them to a single TAR file
-  "Enable folder management":"Yes",
+  "Enable folder management":"No",
   "Compress folders":"No",
 
   # Haplotype retriever and count extractor
diff --git a/parameters_Apollo/sequence_Profiles/sequence_Master.json b/parameters_Apollo/sequence_Profiles/sequence_Master.json
index c34a242..0a7a616 100644
--- a/parameters_Apollo/sequence_Profiles/sequence_Master.json
+++ b/parameters_Apollo/sequence_Profiles/sequence_Master.json
@@ -14,11 +14,11 @@
   "Reinfection availability":"No",
 
   # IF LOCATIONS EQUAL NA THEN NO PROFILES WILL BE CREATED
-  "Fitness profile file":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/sequence_Profiles/profiles/sequence_Fitness_Profile.csv",
-  "Survivability profile file":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/sequence_Profiles/profiles/sequence_Survivability_Profile.csv",
+  "Fitness profile file":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/sequence_Profiles/profiles/sequence_Fitness_Profile.csv",
+  "Survivability profile file":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/sequence_Profiles/profiles/sequence_Survivability_Profile.csv",
 
   "Proof reading availability":"Yes",
-  "Proof reading profile file":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/sequence_Profiles/profiles/sequence_Proof_Reading_Profile.csv",
+  "Proof reading profile file":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/sequence_Profiles/profiles/sequence_Proof_Reading_Profile.csv",
 
   "Recombination availability":"Yes",
 
@@ -32,7 +32,7 @@
 
     "Hotspot 1":{
 
-      "Region":"100_2000",
+      "Region":"5_10",
       # Clock model, can follow a Poisson or Negative Binomial distribution or be Fixed.
       "Clock model":"Poisson",
 
@@ -64,7 +64,7 @@
 
     "Hotspot 2":{
 
-      "Region":"10000_20000",
+      "Region":"25_50",
       # Clock model, can follow a Poisson or Negative Binomial distribution or be Fixed.
       "Clock model":"Negative Binomial",
 
@@ -97,8 +97,8 @@
 
   "Recombination":{
 
-    "Number of hotspots":3,
-    "Recombination profiles folder":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/parameters_Final/sequence_Profiles/recombination_profiles",
+    "Number of hotspots":2,
+    "Recombination profiles folder":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Neutrality_Linux/parameters_Apollo/sequence_Profiles/recombination_profiles",
 
     "Hotspot 1":{
       "Region":"100_200"
@@ -112,11 +112,6 @@
       "Reference selectivity":"1",
     },
 
-    "Hotspot 3":{
-      "Region":"10000_20000"
-      "Reference probability of recombination":"0.05",
-      "Reference selectivity":"1",
-    },
   },
 
 }
diff --git a/simulator_Master.cu b/simulator_Master.cu
index a8e10e4..a87de9f 100644
--- a/simulator_Master.cu
+++ b/simulator_Master.cu
@@ -345,7 +345,7 @@ void simulator_Master::ingress()
 
     network_Manager(functions);
 
-    // exit(-1);
+   // exit(-1);
 
     cout << "STEP 2: Configuring node profiles and within host mechanics\n\n";
     node_Master_Manager(functions);