Merge remote-tracking branch 'firemodels/master' into FireX

Author: cxp484

Source/geom.f90

@@ -41,7 +41,7 @@ MODULE COMPLEX_GEOMETRY
 ! Threshold cut-cell volume ratio used to define very small cut-cells, tied to NOADVANCE.
 REAL(EB), PARAMETER :: MIN_VOL_FACTOR   = 5.E-4_EB
 REAL(EB), PARAMETER :: ADIFF_INFO_FACTOR= 1.E-1_EB
-REAL(EB), PARAMETER :: SNAP_DIST_FACTOR = 1.E-5_EB
+REAL(EB), PARAMETER :: SNAP_DIST_FACTOR = 1.E-4_EB
 REAL(EB), PARAMETER :: MIN_LENGTH_FACTOR= 1.E-2_EB
 
 INTEGER,  SAVE ::      NGUARD = 5        ! Layers of guard-cells.
@@ -206,7 +206,7 @@ MODULE COMPLEX_GEOMETRY
 INTEGER,  ALLOCATABLE, DIMENSION(:,:):: CC_IS_CRS2
 REAL(EB), ALLOCATABLE, DIMENSION(:,:):: CC_SEG_TAN
 INTEGER :: X1NOC, X2NOC, X3NOC
-INTEGER, PARAMETER :: MAX_CELL_POLYLINES =100
+INTEGER, PARAMETER :: MAX_CELL_POLYLINES = 200
 
 REAL(EB):: VAL_TESTX_LOW,VAL_TESTX_HIGH,VAL_TESTY_LOW,VAL_TESTY_HIGH,VAL_TESTZ_LOW,VAL_TESTZ_HIGH
 
@@ -11379,6 +11379,10 @@ SUBROUTINE GET_BODINT_PLANE(X1AXIS,X1PLN,INDX1,PLNORMAL,X2AXIS,X3AXIS,&
 ISEG_NEW = 0
 IF(.NOT.TRI_ONPLANE_ONLY) THEN
    DO ISEG=1,BODINT_PLANE%NSEGS
+       SEG(NOD1:NOD2) = BODINT_PLANE%SEGS(NOD1:NOD2,ISEG)
+       XYZ1(IAXIS:KAXIS) = BODINT_PLANE%XYZ(IAXIS:KAXIS,SEG(NOD1))
+       XYZ2(IAXIS:KAXIS) = BODINT_PLANE%XYZ(IAXIS:KAXIS,SEG(NOD2))
+       IF( NORM2(XYZ2((/X2AXIS,X3AXIS/))-XYZ1((/X2AXIS,X3AXIS/))) < 0.1_EB*GEOMEPS) CYCLE
        IF ( (BODINT_PLANE%SEGTYPE(NOD1,ISEG) == CC_SOLID) .AND. &
             (BODINT_PLANE%SEGTYPE(NOD2,ISEG) == CC_SOLID) ) CYCLE
 

Utilities/Input_Libraries/Chemical_Mechanisms/Cantera/grimech30.spec

@@ -1,54 +1,54 @@
-FORMULA,NAME
-H2,HYDROGEN
-H,HYDROGEN ATOM
-O,OXYGEN ATOM
-O2,OXYGEN
-OH,HYDROXYL RADICAL
-H2O,WATER VAPOR
-HO2,HYDROPEROXY RADICAL
-H2O2,HYDROGEN PEROXIDE
-C,SOOTg
-CH,METHYLIDYNE
-CH2,METHYLENE
-CH2(S),METHYLENEs
-CH3,METHYL RADICAL
-CH4,METHANE
-CO,CARBON MONOXIDE
-CO2,CARBON DIOXIDE
-HCO,FORMYL RADICAL
-CH2O,FORMALDEHYDE
-CH2OH,HYDROXYMETHYL RADICAL
-CH2CHO,VINYLOXY RADICAL
-CH3O,METHOXY RADICAL
-CH3OH,METHANOL
-C2H,ETHYNYL RADICAL
-C2H2,ACETYLENE
-C2H3,VINYL RADICAL
-C2H4,ETHYLENE
-C2H5,ETHYL RADICAL
-C2H6,ETHANE
-HCCO,KETENYL RADICAL
-CH2CO,KETENE
-HCCOH,ETHYNOL
-N,NITROGEN ATOM
-NH,IMIDOGEN
-NNH,NNH
-NH2,DINITROGEN MONOHYDRIDE
-NH3,AMMONIA
-NO,NITRIC OXIDE
-NO2,NITROGEN DIOXIDE
-N2O,NITROUS OXIDE
-HNO,NITROSYL HYDRIDE
-CN,CYANO RADICAL
-HCN,HYDROGEN CYANIDE
-H2CN,METHYLENE-AMIDOGEN
-HCNN,HCNN
-HCNO,FULMINIC ACID
-HOCN,CYANIC ACID
-HNCO,ISOCYANIC ACID
-NCO,ISOCYANATO RADICAL
-N2,NITROGEN
-AR,ARGON
-C3H7,ISOPROPYL RADICAL
-C3H8,PROPANE
-CH3CHO,ETHANAL
+FORMULA,NAME,RADCAL_ID
+H2,HYDROGEN,NONE
+H,HYDROGEN ATOM,NONE
+O,OXYGEN ATOM,NONE
+O2,OXYGEN,NONE
+OH,HYDROXYL RADICAL,NONE
+H2O,WATER VAPOR,WATER VAPOR
+HO2,HYDROPEROXY RADICAL,NONE
+H2O2,HYDROGEN PEROXIDE,NONE
+C,SOOTg,SOOT
+CH,METHYLIDYNE,NONE
+CH2,METHYLENE,NONE
+CH2(S),METHYLENEs,NONE
+CH3,METHYL RADICAL,METHANE
+CH4,METHANE,METHANE
+CO,CARBON MONOXIDE,CARBON DIOXIDE
+CO2,CARBON DIOXIDE,CARBON MONOXIDE
+HCO,FORMYL RADICAL,NONE
+CH2O,FORMALDEHYDE,NONE
+CH2OH,HYDROXYMETHYL RADICAL,NONE
+CH2CHO,VINYLOXY RADICAL,NONE
+CH3O,METHOXY RADICAL,METHANOL
+CH3OH,METHANOL,METHANOL
+C2H,ETHYNYL RADICAL,NONE
+C2H2,ACETYLENE,ETHYLENE
+C2H3,VINYL RADICAL,ETHYLENE
+C2H4,ETHYLENE,ETHYLENE
+C2H5,ETHYL RADICAL,NONE
+C2H6,ETHANE,ETHANE
+HCCO,KETENYL RADICAL,NONE
+CH2CO,KETENE,NONE
+HCCOH,ETHYNOL,NONE
+N,NITROGEN ATOM,NONE
+NH,IMIDOGEN,NONE
+NNH,NNH,NONE
+NH2,DINITROGEN MONOHYDRIDE,NONE
+NH3,AMMONIA,NONE
+NO,NITRIC OXIDE,NONE
+NO2,NITROGEN DIOXIDE,NONE
+N2O,NITROUS OXIDE,NONE
+HNO,NITROSYL HYDRIDE,NONE
+CN,CYANO RADICAL,NONE
+HCN,HYDROGEN CYANIDE,NONE
+H2CN,METHYLENE-AMIDOGEN,NONE
+HCNN,HCNN,NONE
+HCNO,FULMINIC ACID,NONE
+HOCN,CYANIC ACID,NONE
+HNCO,ISOCYANIC ACID,NONE
+NCO,ISOCYANATO RADICAL,NONE
+N2,NITROGEN,NONE
+AR,ARGON,NONE
+C3H7,ISOPROPYL RADICAL,PROPANE
+C3H8,PROPANE,PROPANE
+CH3CHO,ETHANAL,METHANOL

Utilities/Python/scripts/cantera_yaml_2_fds.py

@@ -11,12 +11,14 @@
 parser.add_argument("--yaml_file",help="yaml file",default='noinput',required=True)
 parser.add_argument("--spec_file",help="Cantera to FDS species name lookup csv file (default is yaml_file.spec) with column headings FORMULA and NAME ",default='noinput')
 parser.add_argument("--fds_prop",help="Set to True (default) to use FDS properties when species is in spec_file. ",type=bool,default=True)
+parser.add_argument("--radcal",help="Set to True (default) to use the RADCAL ID in the spec_file. ",type=bool,default=True)
 parser.add_argument("--mf0_file",help="csv file containing MASS_FRACTION_0 with column headings FORMULA and MF0",default='noinput')
 args = parser.parse_args()
 
 yaml_file = args.yaml_file
 bg = args.background
 prop_flag = False
+radcal = True
 spec_data_flag = True
 
 try:
@@ -99,8 +101,11 @@
             write_props = False
       else:
          name = gas.species(i).name
+      if (radcal):
+         radcal_id = spec_data['RADCAL_ID'][spec_index[i]]
    else:
       name = gas.species(i).name
+      radcal = False
    element_list = list(gas.species(i).composition.keys())
    atoms_list = list(gas.species(i).composition.values())
    sigma = gas.species(i).transport.diameter*1E10
@@ -125,7 +130,9 @@
       outstr+="BACKGROUND=T,"
    print(outstr)
    if (write_alt):
-      print("      ALT_ID='"+spec_data['FORMULA'][spec_index[i]]+"'")
+      print("      ALT_ID='"+spec_data['FORMULA'][spec_index[i]]+"',")
+   if (radcal and radcal_id!='NONE'):
+      print("      RADCAL_ID='"+radcal_id+"',")
    if (mf0_index[i]!=-1):
       print("      MASS_FRACTION_0=",mf0_index[i],",")
    if (write_props):