From 159d1527e66157af37baa7e102a9df5b60f14983 Mon Sep 17 00:00:00 2001
From: Jorge Gonzalez <jorge.gonzalez@upm.es>
Date: Tue, 22 Dec 2020 16:52:05 +0100
Subject: [PATCH] Fixed a bug related with reading information on linking
 species.

---
 runs/Argon_Expansion/CX_case.json   | 68 +++++++++++++++++++++++++++++
 runs/Argon_Expansion/base_case.json | 67 ++++++++++++++++++++++++++++
 src/modules/moduleInput.f90         |  2 +
 3 files changed, 137 insertions(+)
 create mode 100644 runs/Argon_Expansion/CX_case.json
 create mode 100644 runs/Argon_Expansion/base_case.json

diff --git a/runs/Argon_Expansion/CX_case.json b/runs/Argon_Expansion/CX_case.json
new file mode 100644
index 0000000..be5d059
--- /dev/null
+++ b/runs/Argon_Expansion/CX_case.json
@@ -0,0 +1,68 @@
+{
+  "output": {
+    "path": "./runs/Argon_Expansion/",
+	"triggerOutput": 10,
+	"cpuTime": false,
+	"numColl": false
+  },
+  "geometry": {
+    "type":     "2DCyl",
+    "meshType": "gmsh",
+    "meshFile": "mesh.msh"
+  },
+  "species": [
+    {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 1.0e8, "ion": "Argon+"},
+    {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "weight": 1.0e8, "neutral": "Argon"}
+  ],
+  "boundary": [ 
+    {"name": "Injection", "physicalSurface": 1, "bTypes": [
+                                                  {"type": "transparent"},
+                                                  {"type": "transparent"}
+                                                 ]},
+    {"name": "Exterior",  "physicalSurface": 2, "bTypes": [
+                                                  {"type": "transparent"},
+                                                  {"type": "transparent"}
+                                                 ]},
+    {"name": "Axis",      "physicalSurface": 3, "bTypes": [
+                                                  {"type": "axis"},
+                                                  {"type": "axis"}
+                                                 ]}
+  ],
+  "inject": [
+    {"name": "Exhausts Ar", "species": "Argon", "flow": 1.7, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
+                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1},
+    {"name": "Exhausts Ar+", "species": "Argon+", "flow": 1.3, "units": "sccm",     "v": 40000.0, "T": [300.0, 300.0, 300.0],
+                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+  ],
+  "reference": {
+    "density": 1.0e19,
+    "mass": 6.633e-26,
+    "temperature": 300.0,
+    "radius": 1.88e-10
+  },
+  "case": {
+    "tau":  [1.0e-4, 1.0e-6],
+    "time": 4.0e-3,
+    "pusher": ["2DCylNeutral", "2DCylNeutral"],
+    "WeightingScheme": "Volume"
+  },
+  "interactions": {
+    "folderCollisions": "./data/collisions/",
+    "collisions": [
+      {"species_i": "Argon", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]},
+      {"species_i": "Argon", "species_j": "Argon+", 
+       "cTypes": [
+         {"type": "elastic",        "crossSection": "EL_Ar-Ar.dat"},
+         {"type": "chargeExchange", "crossSection": "CX_Ar-Ar+.dat"}
+       ]}
+    ]
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 8
+    }
+  }
+}
diff --git a/runs/Argon_Expansion/base_case.json b/runs/Argon_Expansion/base_case.json
new file mode 100644
index 0000000..8483936
--- /dev/null
+++ b/runs/Argon_Expansion/base_case.json
@@ -0,0 +1,67 @@
+{
+  "output": {
+    "path": "./runs/Argon_Expansion/",
+	"triggerOutput": 10,
+	"cpuTime": false,
+	"numColl": false
+  },
+  "geometry": {
+    "type":     "2DCyl",
+    "meshType": "gmsh",
+    "meshFile": "mesh.msh"
+  },
+  "species": [
+    {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 1.0e8, "ion": "Argon+"},
+    {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "weight": 1.0e8, "neutral": "Argon"}
+  ],
+  "boundary": [ 
+    {"name": "Injection", "physicalSurface": 1, "bTypes": [
+                                                  {"type": "transparent"},
+                                                  {"type": "transparent"}
+                                                 ]},
+    {"name": "Exterior",  "physicalSurface": 2, "bTypes": [
+                                                  {"type": "transparent"},
+                                                  {"type": "transparent"}
+                                                 ]},
+    {"name": "Axis",      "physicalSurface": 3, "bTypes": [
+                                                  {"type": "axis"},
+                                                  {"type": "axis"}
+                                                 ]}
+  ],
+  "inject": [
+    {"name": "Exhausts Ar", "species": "Argon", "flow": 1.7, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
+                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1},
+    {"name": "Exhausts Ar+", "species": "Argon+", "flow": 1.3, "units": "sccm",     "v": 40000.0, "T": [300.0, 300.0, 300.0],
+                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+  ],
+  "reference": {
+    "density": 1.0e19,
+    "mass": 6.633e-26,
+    "temperature": 300.0,
+    "radius": 1.88e-10
+  },
+  "case": {
+    "tau":  [1.0e-4, 1.0e-6],
+    "time": 4.0e-3,
+    "pusher": ["2DCylNeutral", "2DCylNeutral"],
+    "WeightingScheme": "Volume"
+  },
+  "interactions": {
+    "folderCollisions": "./data/collisions/",
+    "collisions": [
+      {"species_i": "Argon", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]},
+      {"species_i": "Argon", "species_j": "Argon+", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]}
+    ]
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 8
+    }
+  }
+}
diff --git a/src/modules/moduleInput.f90 b/src/modules/moduleInput.f90
index 2b5c2c1..5dd69e1 100644
--- a/src/modules/moduleInput.f90
+++ b/src/modules/moduleInput.f90
@@ -279,6 +279,8 @@ MODULE moduleInput
 
       !Reads relations between species
       DO i = 1, nSpecies
+        WRITE(iString, '(I2)') i
+        object = 'species(' // TRIM(iString) // ')'
         SELECT TYPE(sp => species(i)%obj)
         TYPE IS (speciesNeutral)
           !Gets species linked ion