diff --git a/examples/SedovBlast_3D/run.sh b/examples/SedovBlast_3D/run.sh
index 00d5e5b91c31e64f824a3d2a28c8e1a126684a74..590ed5efa7dfd4ed7677f3eb9627d1139d20fc8b 100755
--- a/examples/SedovBlast_3D/run.sh
+++ b/examples/SedovBlast_3D/run.sh
@@ -12,6 +12,9 @@ then
python makeIC.py
fi
+# Generate output fields
+../create_ouput_fields.py ../../config.h -o output_fields.yml -d ../output_fields_examples/
+
# Run SWIFT
../swift -s -t 4 sedov.yml 2>&1 | tee output.log
diff --git a/examples/SedovBlast_3D/sedov.yml b/examples/SedovBlast_3D/sedov.yml
index 5368c02645af9a170e0401c6772532ed4b689e77..d73f70be0b5b708f0b2bed80122d1cabab6e5d72 100644
--- a/examples/SedovBlast_3D/sedov.yml
+++ b/examples/SedovBlast_3D/sedov.yml
@@ -19,7 +19,7 @@ Snapshots:
time_first: 0. # Time of the first output (in internal units)
delta_time: 1e-2 # Time difference between consecutive outputs (in internal units)
compression: 4
- FieldsFilename: ../output_fields_example.yml
+ FieldsFilename: output_fields.yml
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/create_ouput_fields.py b/examples/create_ouput_fields.py
new file mode 100644
index 0000000000000000000000000000000000000000..86ca8a585dfc1ed5af85b8b6b4c0bf9a0cdf9451
--- /dev/null
+++ b/examples/create_ouput_fields.py
@@ -0,0 +1,291 @@
+#!/usr/bin/env python3
+
+from optparse import OptionParser
+from regex import search
+from os import path, remove
+
+# fields to do
+todo = [
+ "chemistry", "cooling",
+ "gravity", "stars",
+ "hydro"]
+
+# number of particle type
+N_type = 6
+
+
+def parseOptions():
+ """
+ Parse options.
+
+ Returns
+ -------
+
+ opt:
+ Option structure
+
+ args:
+ Arguments
+ """
+ usage = """usage: %prog [options] args1
+ If options are not provided, this script will read the config.h file \
+provided (args1) and use theses values.
+ """
+
+ parser = OptionParser(usage=usage)
+
+ parser.add_option("--with-cooling",
+ dest="cooling",
+ help="Cooling Type",
+ default="",
+ type=str,
+ metavar="STR")
+
+ parser.add_option("--with-chemistry",
+ dest="chemistry",
+ help="Chemistry Type",
+ default="",
+ type=str,
+ metavar="STR")
+
+ parser.add_option("--with-hydro",
+ dest="hydro",
+ help="Hydro Type",
+ default="",
+ type=str,
+ metavar="STR")
+
+ parser.add_option("--with-stars",
+ dest="stars",
+ help="Stars Type",
+ default="default",
+ type=str,
+ metavar="STR")
+
+ parser.add_option("--with-gravity",
+ dest="gravity",
+ help="Gravity Type",
+ default="default",
+ type=str,
+ metavar="STR")
+
+ parser.add_option("-o", "--output",
+ dest="o",
+ help="Output filename",
+ type=str,
+ default=None,
+ metavar="STR")
+
+ parser.add_option("-d", "--example_directory",
+ dest="d",
+ help="Directory containing the examples",
+ type=str,
+ default=None,
+ metavar="STR")
+
+ return parser.parse_args()
+
+
+def readConfig(filename):
+ """
+ Read the config.h file and parse it to keep
+ only the definitions.
+
+ Parameters
+ ----------
+
+ filename: str
+ Filename to parse
+
+ Returns
+ -------
+
+ options: list
+ List of options
+ """
+ expression = "#define (.*) 1"
+ options = []
+ with open(filename, "r") as f:
+ for line in f:
+ tmp = search(expression, line)
+ if tmp is not None:
+ options.append(tmp.group(1))
+
+ return options
+
+
+def getConfig(opt, swift_options, current):
+ """
+ Parse the config.h options and extract the required
+ parameter. If not able to find an option, return False
+
+ Parameters
+ ----------
+
+ opt:
+ Option structure
+
+ swift_options: list
+ Option in config.h
+
+ current: str
+ Current option
+
+ Returns
+ -------
+
+ option: str
+ name of the option (in lower case)
+ """
+ # if given in options, returns
+ if getattr(opt, current) != "":
+ return getattr(opt, current)
+
+ # get current option
+ caps = current.upper()
+ expression = "%s_(.*)" % caps
+ if current == "hydro":
+ expression = "(.*)_SPH"
+ for i in swift_options:
+ tmp = search(expression, i)
+ if tmp is not None:
+ return tmp.group(1).lower()
+ return False
+
+
+def readYamlFile(filename):
+ """
+ Read quickly a yaml file.
+
+ Parameters
+ ----------
+
+ filename: str
+ file to read
+
+ Returns
+ -------
+
+ d: dict
+ key -> section name, value -> list of parameters
+ """
+ d = {}
+ key = None
+ section = "(PartType\d+):"
+ with open(filename, "r") as f:
+ for line in f:
+ # check for section
+ tmp = search(section, line)
+ if tmp is not None:
+ key = tmp.group(1)
+ d[key] = []
+ continue
+
+ # skip if not a parameter or outside
+ # a section
+ if ":" not in line or key is None:
+ continue
+
+ # ensure end of line
+ if "\n" not in line:
+ line += "\n"
+
+ # write line
+ d[key].append(line)
+
+ return d
+
+
+def generateFile(opt):
+ """
+ Generate an output fields file from examples.
+
+ Parameters
+ ----------
+
+ opt:
+ Option structure
+
+ Returns
+ -------
+
+ d: dict
+ key -> section name, value -> list of parameters
+ """
+ d = {}
+ # read all files
+ for current in todo:
+ filename = current + "_" + getattr(opt, current) + ".yml"
+ filename = opt.d + "/" + filename
+ data = readYamlFile(filename)
+
+ for tpe in range(N_type):
+ name = "PartType%i" % tpe
+ if name not in data:
+ continue
+
+ if name not in d:
+ d[name] = data[name]
+
+ else:
+ d[name].extend(data[name])
+ return d
+
+
+def writeOutputFields(d, opt):
+ """
+ Write the output.
+
+ Parameters
+ ----------
+
+ d: dict
+ key -> section name, value -> list of parameters
+
+ opt:
+ Option structure
+
+ """
+ with open(opt.o, "w") as f:
+ for tpe in range(N_type):
+ name = "PartType%i" % tpe
+ if name not in d:
+ continue
+ f.write("%s:\n" % name)
+ for i in d[name]:
+ f.write(i)
+
+ f.write("\n")
+
+
+if __name__ == "__main__":
+ # parse option
+ opt, args = parseOptions()
+
+ # check inputs
+ # arguments
+ if len(args) != 1:
+ raise IOError("A file should be provided")
+ filename = args[0]
+
+ # output file
+ if opt.o is None:
+ raise IOError("The output option '-o' is required")
+
+ # example directory
+ if opt.d is None:
+ raise IOError("The example directory option '-d' is required")
+
+ # read configuration file
+ swift_options = readConfig(filename)
+
+ # get correct configuration
+ for current in todo:
+ tmp = getConfig(opt, swift_options, current)
+ if tmp is False:
+ raise IOError("Unable to get field %s" % current)
+ setattr(opt, current, tmp)
+
+ # generate and write output_fields file
+ d = generateFile(opt)
+ writeOutputFields(d, opt)
diff --git a/examples/main.c b/examples/main.c
index 605b2d330795543c0dcf4c4ca915798bd75aeb48..ec0787bfd394b00bdf2eb91ed5e559d42f8fb677 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -469,11 +469,8 @@ int main(int argc, char *argv[]) {
if (myrank == 0) {
message("Reading runtime output fields from file '%s'",
outputFieldsFileName);
- if (strcmp(outputFieldsFileName, "") != 0)
- parser_read_file(outputFieldsFileName, output_fields);
- else
- parser_init(outputFieldsFileName, output_fields);
-
+ parser_read_file(outputFieldsFileName, output_fields);
+
/* And dump the parameters as used. */
parser_write_params_to_file(output_fields, "used_output_fields.yml");
}
diff --git a/examples/output_fields_example.yml b/examples/output_fields_example.yml
deleted file mode 100644
index 22dfdc35a91efeabdc96fbdcb92dfa65fbc191b8..0000000000000000000000000000000000000000
--- a/examples/output_fields_example.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-# Gas
-PartType0:
- Coordinates: 1 # Request to write output
- Masses: 1
- Velocities: 1
- SmoothingLength: 1
- Entropy: 1
- ParticleIDs: 1
- Density: 1
- InternalEnergy: 0 # Request to not write output
- Pressure: 0
- Potential: 0
-
-# Dark Matter
-PartType1:
- Coordinates: 1
- Velocities: 1
- Masses: 1
- ParticleIDs: 1
- Potential: 0
-
-# Stars
-PartType2:
- Coordinates: 1
- Velocities: 1
- Masses: 1
- ParticleIDs: 1
\ No newline at end of file
diff --git a/examples/output_fields_examples/chemistry_eagle.yml b/examples/output_fields_examples/chemistry_eagle.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d62c2b32d2972f233fe7a3962d7b980c9e5007ce
--- /dev/null
+++ b/examples/output_fields_examples/chemistry_eagle.yml
@@ -0,0 +1,14 @@
+# gas
+PartType0:
+ ElementAbundance: 1
+ SmoothedElementAbundance: 1
+ Metallicity: 1
+ SmoothedMetallicity: 1
+ TotalMassFromSNIa: 1
+ MetalMassFracFromSNIa: 1
+ TotalMassFromAGB: 1
+ MetalMassFracFromAGB: 1
+ TotalMassFromSNII: 1
+ MetalMassFracFromSNII: 1
+ IronMassFracFromSNIa: 1
+ SmoothedIronMassFracFromSNIa: 1
\ No newline at end of file
diff --git a/examples/output_fields_examples/chemistry_gear.yml b/examples/output_fields_examples/chemistry_gear.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a64dbfb0152a399a163e44c4a954cad7c3f887d8
--- /dev/null
+++ b/examples/output_fields_examples/chemistry_gear.yml
@@ -0,0 +1,4 @@
+# gas
+PartType0:
+ SmoothedElementAbundance: 1
+ ElementAbundance: 1
\ No newline at end of file
diff --git a/examples/output_fields_examples/chemistry_none.yml b/examples/output_fields_examples/chemistry_none.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/output_fields_examples/cooling_const_du.yml b/examples/output_fields_examples/cooling_const_du.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/output_fields_examples/cooling_eagle.yml b/examples/output_fields_examples/cooling_eagle.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/output_fields_examples/cooling_grackle.yml b/examples/output_fields_examples/cooling_grackle.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/output_fields_examples/cooling_lambda.yml b/examples/output_fields_examples/cooling_lambda.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/output_fields_examples/cooling_none.yml b/examples/output_fields_examples/cooling_none.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/output_fields_examples/gravity_default.yml b/examples/output_fields_examples/gravity_default.yml
new file mode 100644
index 0000000000000000000000000000000000000000..26e54f1fa0ca9b4679c967891c3019fe69e55c6b
--- /dev/null
+++ b/examples/output_fields_examples/gravity_default.yml
@@ -0,0 +1,7 @@
+# Dark Matter
+PartType1:
+ Coordinates: 1
+ Velocities: 1
+ Masses: 1
+ ParticleIDs: 1
+ Potential: 1
diff --git a/examples/output_fields_examples/hydro_default.yml b/examples/output_fields_examples/hydro_default.yml
new file mode 100644
index 0000000000000000000000000000000000000000..350979d7aa60bb868afd195653599945bdc910c7
--- /dev/null
+++ b/examples/output_fields_examples/hydro_default.yml
@@ -0,0 +1,10 @@
+# Gas
+PartType0:
+ Coordinates: 1
+ Masses: 1
+ Velocities: 1
+ SmoothingLength: 1
+ ParticleIDs: 1
+ Density: 1
+ InternalEnergy: 1
+ Potential: 1
diff --git a/examples/output_fields_examples/hydro_gadget2.yml b/examples/output_fields_examples/hydro_gadget2.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9cfcf123df4f8f1a85123069505ca6e6275e0547
--- /dev/null
+++ b/examples/output_fields_examples/hydro_gadget2.yml
@@ -0,0 +1,17 @@
+# Gas
+PartType0:
+ Coordinates: 1
+ Masses: 1
+ Velocities: 1
+ SmoothingLength: 1
+ Entropy: 1
+ ParticleIDs: 1
+ Density: 1
+ InternalEnergy: 1
+ Pressure: 1
+ Potential: 1
+ # debug fields
+ # Num_ngb_density: 0
+ # Num_ngb_force: 0
+ # Ids_ngb_density: 0
+ # Ids_ngb_force
\ No newline at end of file
diff --git a/examples/output_fields_examples/hydro_gizmo.yml b/examples/output_fields_examples/hydro_gizmo.yml
new file mode 100644
index 0000000000000000000000000000000000000000..17f4231d638ef6eac4ec062f12c6dcaacab5dd80
--- /dev/null
+++ b/examples/output_fields_examples/hydro_gizmo.yml
@@ -0,0 +1,13 @@
+# Gas
+PartType0:
+ Coordinates: 1
+ Masses: 1
+ Velocities: 1
+ SmoothingLength: 1
+ Entropy: 1
+ ParticleIDs: 1
+ Density: 1
+ InternalEnergy: 1
+ Pressure: 1
+ TotEnergy: 1
+ Potential: 1
diff --git a/examples/output_fields_examples/hydro_minimal.yml b/examples/output_fields_examples/hydro_minimal.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bbc1ae9371f2cc6d564e293236270f1698e31984
--- /dev/null
+++ b/examples/output_fields_examples/hydro_minimal.yml
@@ -0,0 +1,12 @@
+# Gas
+PartType0:
+ Coordinates: 1
+ Masses: 1
+ Velocities: 1
+ SmoothingLength: 1
+ Entropy: 1
+ ParticleIDs: 1
+ Density: 1
+ InternalEnergy: 1
+ Pressure: 1
+ Potential: 1
diff --git a/examples/output_fields_examples/hydro_pressureentropy.yml b/examples/output_fields_examples/hydro_pressureentropy.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b4ea000c11fb5c23e6034bef4ccf090d935e1261
--- /dev/null
+++ b/examples/output_fields_examples/hydro_pressureentropy.yml
@@ -0,0 +1,13 @@
+# Gas
+PartType0:
+ Coordinates: 1
+ Masses: 1
+ Velocities: 1
+ SmoothingLength: 1
+ Entropy: 1
+ ParticleIDs: 1
+ Density: 1
+ InternalEnergy: 1
+ Pressure: 1
+ Potential: 1
+ WeightedDensity: 1
\ No newline at end of file
diff --git a/examples/output_fields_examples/hydro_shadowswift.yml b/examples/output_fields_examples/hydro_shadowswift.yml
new file mode 100644
index 0000000000000000000000000000000000000000..edd62d19aea73e80bfb1c4cec663ca4277a38d88
--- /dev/null
+++ b/examples/output_fields_examples/hydro_shadowswift.yml
@@ -0,0 +1,16 @@
+# Gas
+PartType0:
+ Coordinates: 1
+ Masses: 1
+ Velocities: 1
+ SmoothingLength: 1
+ Entropy: 1
+ ParticleIDs: 1
+ Density: 1
+ InternalEnergy: 1
+ Pressure: 1
+ Potential: 1
+ Acceleration: 1
+ Volume: 1
+ GradDensity: 1
+ TotEnergy: 1
\ No newline at end of file
diff --git a/examples/output_fields_examples/stars_default.yml b/examples/output_fields_examples/stars_default.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bc447626dda7f394f7d6a4be677cd23ad680db85
--- /dev/null
+++ b/examples/output_fields_examples/stars_default.yml
@@ -0,0 +1,6 @@
+# Stars
+PartType2:
+ Coordinates: 1
+ Velocities: 1
+ Masses: 1
+ ParticleIDs: 1
\ No newline at end of file