Dummy PR for importing manifold stuff

Exec/RegTests/EnclosedFlame/GNUmakefile

@@ -1,16 +1,15 @@
-TOP = ../../../..
+TOP = ../../../Submodules
 AMREX_HOME         ?= ${TOP}/amrex
-PELELMEX_HOME      ?= ${TOP}/PeleLMeX
+PELELMEX_HOME      ?= ${TOP}/..
 PELE_PHYSICS_HOME  ?= ${TOP}/PelePhysics
 AMREX_HYDRO_HOME   ?= ${TOP}/AMReX-Hydro
 
-
 # AMReX
 DIM             = 2
 DEBUG           = FALSE
 PRECISION       = DOUBLE
 VERBOSE         = FALSE
-TINY_PROFILE    = FALSE
+TINY_PROFILE    = TRUE
 
 # Compilation
 COMP            = gnu
@@ -21,9 +20,19 @@ USE_HIP         = FALSE
 
 # PeleLMeX
 
+FUEGO_GAS       = FALSE
 # PelePhysics
-Chemistry_Model = drm19
-Eos_Model		= Fuego
-Transport_Model = Simple
+ifeq ($(FUEGO_GAS), TRUE)
+	Chemistry_Model = posf10325
+	Eos_Model	= Fuego
+	Transport_Model = Simple
+else
+	USE_LIBTORCH    = FALSE
+	LIBTORCH_HOME = /home/bperry/libtorch
+	DEFINES += -D_GLIBCXX_USE_CXX11_ABI=0
+	Eos_Model = Manifold
+	Chemistry_Model = Manifold2d
+	Transport_Model = Manifold
+endif
 
 include $(PELELMEX_HOME)/Utils/Make.PeleLMeX

Exec/RegTests/EnclosedFlame/README

@@ -0,0 +1,39 @@
+Stuff that needs to be done to run this case
+
+-- COMPILE --
+make TPL -j
+make -j
+
+-- Generate Turbulence initial condition --
+python gen_hit_ic.py -k0 4 -N 128
+
+-- Run --
+srun -n 36 PeleLMeX2d.gnu.TPROF.MPI.ex input.nn
+
+
+#### NOTES ####
+Contained are files to run with an FGM+ANN model trained on a 1D premixed flame
+and a CMLM model trained from corresponding 3D DNS
+
+Required files include a pmf data file used to set the initial condition.
+In the input.nn file, set either
+
+   pmf.datafile =  "prem_posf10325_phi1_p1_t298_mani_cmlm.dat"
+-- OR --
+   pmf.datafile =  "prem_posf10325_phi1_p1_t298_mani_fgm.dat"
+
+Also required are a neural network file and info file.
+In the input.nn file, set either
+
+   manifold.filename = cmlm_net.pnn
+   manifold.info_filename = cmlm_net_info.txt
+-- OR --
+   manifold.filename = fgm_net.pnn
+   manifold.info_filename = fgm_net_info.txt
+
+Note that the CMLM model is a 2D manifold while the FGM one is a 1D manifold.
+This means the correct setting must be used in the GNUmakefile when compiling:
+
+   Chemistry_Model = Manifold2d
+-- OR --
+   Chemistry_Model = Manifold

Exec/RegTests/EnclosedFlame/cmlm_net_info.txt

@@ -0,0 +1,22 @@
+# Name of the neural network model
+model_name = cmlm_dns
+# Number of input dimensions
+ndim = 2
+# Number of output dimensions
+nvar = 17
+# Number of manifold parameters
+nmanpar = 2
+# Names of input variables
+dimnames = xi0 xi1
+# Names of output variables
+varnames = Y-CO2 Y-CO Y-CH2O SRC_H2O SRC_H2 SRC_CO2 SRC_CO SRC_POSF10325 SRC_O2 T RHO lnRHO \
+           invRHO DIFF VISC SRC_xi0 SRC_xi1
+# Definitions of input variables
+def_xi0 = 22.34722900390625*Y-CO2 -396.7853088378906*Y-H2 53.42775344848633*Y-N2 \
+          23.05693817138672*Y-CO 3.7954090657876804e-05*Y-O2 5.909298488404602e-05*Y-H2O \
+          -8.786284161033109e-05*Y-POSF10325
+def_xi1 = 2.3632654119865038e-05*Y-CO2 -0.5249142050743103*Y-H2 28.18173599243164*Y-N2 \
+          -29.479734420776367*Y-CO -4.5221535401651636e-05*Y-O2 71.97798156738281*Y-H2O \
+          -3.83632504963316e-05*Y-POSF10325
+# Biases to be used calculating input variables
+manibiases = -40.21234130859375 -22.204334259033203

Exec/RegTests/EnclosedFlame/fgm_net_info.txt

@@ -0,0 +1,18 @@
+# Name of the neural network model
+model_name = premixed
+# Number of input dimensions
+ndim = 1
+# Number of output dimensions
+nvar = 15
+# Number of manifold parameters
+nmanpar = 1
+# Names of input variables
+dimnames = xi0
+# Names of output variables
+varnames = Y-CO2 Y-CO Y-CH2O SRC_H2O SRC_H2 SRC_CO2 SRC_CO SRC_POSF10325 SRC_O2 T RHO lnRHO DIFF \
+           VISC SRC_xi0
+# Definitions of input variables
+def_xi0 = 15.390820503234863*Y-CO2 15.390820503234863*Y-H2 0.0*Y-N2 15.390819549560547*Y-CO \
+          0.0*Y-O2 15.390820503234863*Y-H2O 0.0*Y-POSF10325
+# Biases to be used calculating input variables
+manibiases = -2.206676721572876