FireX: Merge with firemodels/master

Manuals/Bibliography/commoncommands.tex

@@ -73,7 +73,7 @@
     tabsize=4,
     rulecolor=,
     language=Fortran,
-        basicstyle=\footnotesize\ttfamily,
+        basicstyle=\small\ttfamily,
         upquote=true,
         aboveskip={\baselineskip},
         belowskip={\baselineskip},

Manuals/FDS_User_Guide/FDS_User_Guide.tex

@@ -1029,7 +1029,6 @@ \subsection{Multiple Meshes}
 
 For cases involving many meshes, you might want to assign them colors using either the character string \ct{COLOR} or the integer triplet \ct{RGB}. You may also want to consider using the multiplying feature to easily create a 3-D array of meshes. See Sec.~\ref{info:MULT} for details.
 
-One other useful parameter for larger MPI jobs is called \ct{VERBOSE} on the \ct{MISC} line. This logical parameter suppresses information related to MPI process and OpenMP thread assignments that is printed to the diagnostic output files. By default, its value is \ct{T} for MPI jobs involving 50 or less processes, and \ct{F} for larger jobs.
 
 
 \subsection{Mesh Alignment}
@@ -11877,7 +11876,8 @@ \chapter{Alphabetical List of Input Parameters}
 % ignorenamelistkw: /MISC/STRATIFICATION, /MISC/SUPPRESSION, /MISC/UVW_FILE, /MISC/TENSOR_DIFFUSIVITY
 % ignorenamelistkw: /MISC/CC_IBM, /MISC/CCVOL_LINK, /MISC/TEST_NEW_CHAR_MODEL, /MISC/FLUX_LIMITER_MW_CORRECTION
 % ignorenamelistkw: /PART/DEBUG, /PART/EMBER_SNAG_FACTOR
-% ignorenamelistkw: /REAC/C, /REAC/H, /REAC/O, /REAC/N, /REAC/FORMULA,
+% ignorenamelistkw: /PRES/WRITE_PARCSRPCG_MATRIX
+% ignorenamelistkw: /REAC/C, /REAC/H, /REAC/O, /REAC/N, /REAC/FORMULA
 % ignorenamelistkw: /SLCF/DEBUG, /SLCF/RLE_MIN, /SLCF/RLE_MAX, /SLCF/SLICETYPE
 % ignorenamelistkw: /SURF/MOISTURE_FRACTION
 % ignorenamelistkw: /TIME/RAMP_DT
@@ -12805,7 +12805,7 @@ \section{\texorpdfstring{{\tt MISC}}{MISC} (Miscellaneous Parameters)}
 \ct{TURBULENCE_MODEL}                             & Character    & Section~\ref{info:LES}                  &            & \ct{'DEARDORFF'} \\ \hline
 \ct{TURBULENT_DEPOSITION}                         & Logical      & Section~\ref{info:deposition}           &            & \ct{T}           \\ \hline
 \ct{UNFREEZE_TIME}                               & Real          & Section~\ref{info:FREZ}                 &            &                  \\ \hline
-\ct{VERBOSE}                                       & Logical      & Section~\ref{info:multimesh}            &            &                   \\ \hline
+\ct{VERBOSE}                                       & Logical      & Section~\ref{out:file}                  &            & \ct{F}            \\ \hline
 \ct{VISIBILITY_FACTOR}                            & Real         & Section~\ref{info:visibility}           &            & 3                 \\ \hline
 \ct{VN_MAX}                                       & Real         & Section~\ref{info:VN}                   &            & 1.0               \\ \hline
 \ct{VN_MIN}                                       & Real         & Section~\ref{info:VN}                   &            & 0.8               \\ \hline
@@ -14613,6 +14613,9 @@ \section{Diagnostic Output ({\tt .out})}
 
 Following the completion of a successful run, a summary of the CPU usage per subroutine is listed in the file called \ct{CHID_cpu.csv} (Section~\ref{out:CPU}). This is useful in determining where most of the computational effort is being placed.
 
+Add \ct{VERBOSE=T} to the \ct{MISC} line to add addiational information about time usage to the diagnostic file.
+
+
 \section{Heat Release Rate and Related Quantities (\ct{_hrr.csv})}
 \label{out:hrr}
 
@@ -14696,96 +14699,6 @@ \section{CPU Usage Data}
 \section{Time Step Data}
 \label{out:timestep}
 
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
-The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
-\begin{lstlisting}
-Time Step,Wall Time,Step Size,Simulation Time,CPU Time
-\end{table}
-
-The \ct{CHID_cpu.csv} file is printed out at the end of the simulation. To force it to be printed out periodically during the simulation, set \ct{DT_CPU} or \ct{RAMP_CPU} on the \ct{DUMP} line. The latter parameter allows you to write out the files at specified times.
-
-\section{Time Step Data}
-\label{out:timestep}
-
 The file called \ct{CHID_steps.csv} records data on the size of time steps and the amount of elapsed CPU time.
 \begin{lstlisting}
 Time Step,Wall Time,Step Size,Simulation Time,CPU Time

Source/chem.f90

@@ -101,7 +101,7 @@ SUBROUTINE DERIVATIVE(CVEC,FVEC, TN, USER_DATA)
           K_0, K_INF, P_RI, FCENT, B_I, RRTMP, THIRD_BODY_ENHANCEMENT, PR
 INTEGER :: I,NS, ITMP
 REAL(EB) :: ZZ(N_TRACKED_SPECIES), CP, HS_I, DG, TMPI
-REAL(EB) :: ZETA, MIXING_FACTOR, VOL_CHANGE_TERM, SUM_OMEGA_DOT, SUM_CC, MW0, MW, SUM_H_ZZ0
+REAL(EB) :: ZETA, MIXING_FACTOR, VOL_CHANGE_TERM, SUM_OMEGA_DOT, SUM_CC, MW0, MW, SUM_H_ZZ0, EXPONENT, CONC
 TYPE(REACTION_TYPE), POINTER :: RN
 
 TMP = MAX(CVEC(N_TRACKED_SPECIES+1), MIN_CHEM_TMP)
@@ -144,7 +144,14 @@ SUBROUTINE DERIVATIVE(CVEC,FVEC, TN, USER_DATA)
    ! MULTIPLY WITH MOLAR_CONCENTRATION ^ STOICHIOMETRIC_COEFF
    DO NS=1,RN%N_SPEC
       IF (CVEC(YP2ZZ(RN%N_S_INDEX(NS))) < MIN_SPEC(YP2ZZ(RN%N_S_INDEX(NS)))) CYCLE REACTION_LOOP
-      R_F = R_F*(CVEC(YP2ZZ(RN%N_S_INDEX(NS))))**RN%N_S(NS) 
+      EXPONENT = RN%N_S(NS)
+      CONC = CVEC(YP2ZZ(RN%N_S_INDEX(NS)))
+      IF (EXPONENT < 1._EB) THEN
+         R_F = R_F * CONC**(EXPONENT - 1._EB)
+         R_F = R_F * CONC
+      ELSE
+          R_F = R_F * CONC**EXPONENT
+      END IF
    ENDDO
 
    ! CALCULATE B_I BASED ON TYPE OF REACTION
@@ -207,7 +214,6 @@ SUBROUTINE DERIVATIVE(CVEC,FVEC, TN, USER_DATA)
 ! PRESSURE DERIVATIVE (CONSTANT PRESSURE ASSUMPTION)
 FVEC(N_TRACKED_SPECIES+2) = 0._EB
 
-
 END SUBROUTINE DERIVATIVE
 
 
@@ -336,11 +342,11 @@ SUBROUTINE JACOBIAN(CVEC,FVEC,JMAT,TN,USER_DATA)
 
 REAL(EB) :: R_F,DCVEC1,DCVEC2, MIN_SPEC(N_TRACKED_SPECIES), KG,  TMP, RHO, &
             K_0, K_INF, P_RI, FCENT, B_I, RRTMP, THIRD_BODY_ENHANCEMENT, PR
-REAL(EB) :: ZZ(N_TRACKED_SPECIES), CP_I(N_TRACKED_SPECIES), HS_I(N_TRACKED_SPECIES)    
+REAL(EB) :: ZZ(N_TRACKED_SPECIES), CP_I(N_TRACKED_SPECIES), HS_I(N_TRACKED_SPECIES)
 REAL(EB) :: DKCDTBYKC, DBIDC(N_TRACKED_SPECIES), DBIDT, CP, DCPDT, DKINFDTMPBYKINF, DTMPDT, DG, TMPI, RHOI, CPI
 REAL(EB) :: ZETA, MIXING_FACTOR, SUM_OMEGA_DOT, SUM_CC, SUM_OMEGA_DOT_BY_CC, SUM_CC_I, ENRG_TERM, DUMMY1, DUMMY2, DUMMY3
 REAL(EB) :: VOL_CHANGE_TERM1, VOL_CHANGE_TERM2, VOL_CHANGE_TERM3, VOL_CHANGE_TERM, SUM_DOMEGA_DOT_BY_DT, MW0, MW, &
-            SUM_CP_ZZ0,SUM_H_ZZ0
+            SUM_CP_ZZ0,SUM_H_ZZ0, EXPONENT, CONC, CONC_EXP
 INTEGER :: I,NS, NS1, NS2, ITMP
 TYPE(REACTION_TYPE), POINTER :: RN
 
@@ -391,10 +397,8 @@ SUBROUTINE JACOBIAN(CVEC,FVEC,JMAT,TN,USER_DATA)
       DKCDTBYKC = ((RN%DELTA_G(MIN(I_MAX_TEMP,NINT(TMP)))*TMPI + RN%DELTA_S(MIN(I_MAX_TEMP,NINT(TMP))))+RN%C0_EXP)*TMPI 
    ENDIF
 
-   ! MULTIPLY WITH MOLAR_CONCENTRATION ^ STOICHIOMETRIC_COEFF
    DO NS=1,RN%N_SPEC
       IF (CVEC(YP2ZZ(RN%N_S_INDEX(NS))) < MIN_SPEC(YP2ZZ(RN%N_S_INDEX(NS)))) CYCLE REACTION_LOOP
-      R_F = R_F*(CVEC(YP2ZZ(RN%N_S_INDEX(NS))))**RN%N_S(NS)
    ENDDO
 
 
@@ -431,13 +435,41 @@ SUBROUTINE JACOBIAN(CVEC,FVEC,JMAT,TN,USER_DATA)
 
    !Contribution of qi
    DO NS1 = 1, RN%N_SPEC
+      ! MULTIPLY WITH MOLAR_CONCENTRATION ^ STOICHIOMETRIC_COEFF
+      CONC_EXP = 1.0_EB
+      DO NS2=1,RN%N_SPEC
+         EXPONENT = RN%N_S(NS2)
+         CONC = CVEC(YP2ZZ(RN%N_S_INDEX(NS2)))
+         IF (NS2 == NS1) THEN
+            CONC_EXP = CONC_EXP * MERGE((CONC+TWO_EPSILON_EB)**(EXPONENT - 1._EB), CONC**(EXPONENT - 1._EB), EXPONENT < 1._EB)
+         ELSE
+            IF (EXPONENT < 1._EB) THEN
+               CONC_EXP = CONC_EXP * CONC * (CONC+TWO_EPSILON_EB)**(EXPONENT - 1._EB)
+            ELSE
+               CONC_EXP = CONC_EXP * CONC**EXPONENT
+            END IF
+         ENDIF
+      ENDDO
+
       DO NS=1,RN%N_SMIX_FR
-         DCVEC1 = R_F*RN%NU_NN(RN%NU_INDEX(NS))*RN%N_S(NS1)/CVEC(YP2ZZ(RN%N_S_INDEX(NS1)))
+         DCVEC1 = R_F*CONC_EXP*RN%NU_NN(RN%NU_INDEX(NS))*RN%N_S(NS1)
          JMAT((YP2ZZ(RN%N_S_INDEX(NS1))),RN%NU_INDEX(NS)) = &
          JMAT((YP2ZZ(RN%N_S_INDEX(NS1))),RN%NU_INDEX(NS))+ DCVEC1 
       ENDDO   
    ENDDO 
 
+   ! CALCULATE THE REACTION RATE
+   DO NS=1,RN%N_SPEC
+      EXPONENT = RN%N_S(NS)
+      CONC = CVEC(YP2ZZ(RN%N_S_INDEX(NS)))
+      IF (EXPONENT < 1._EB) THEN
+         R_F = R_F * CONC**(EXPONENT - 1._EB)
+         R_F = R_F * CONC
+      ELSE
+          R_F = R_F * CONC**EXPONENT
+      END IF
+   ENDDO
+
    ! Add contribution of C_I
    IF (RN%THIRD_BODY) THEN
       DO NS = 1,N_TRACKED_SPECIES
@@ -792,6 +824,7 @@ SUBROUTINE CVODE_SERIAL(CC,ZZ_0, TMP_IN, PR_IN, ZETA0, TAU_MIX, CELL_MASS, TCUR,
 REAL(C_DOUBLE)                 :: CVEC_C(N_TRACKED_SPECIES+2)    ! N_SP + 2 (FOR TEMPERATURE AND PRESSURE)
 REAL(C_DOUBLE)                 :: ATOLVEC_C(N_TRACKED_SPECIES+2) ! N_SP + 2 
 INTEGER(C_LONG)                :: MAXSTEPS_C     ! MAXIMUM NUMBER OF INTERNAL STEPS
+INTEGER(C_INT)                 :: MAXORD_C       ! Maximum number of order.
 INTEGER(C_INT64_T)             :: NEQ
 REAL(C_DOUBLE)                 :: CHEM_TIME_C(1)    ! OUTPUT CHEMICAL TIME
 
@@ -890,6 +923,15 @@ SUBROUTINE CVODE_SERIAL(CC,ZZ_0, TMP_IN, PR_IN, ZETA0, TAU_MIX, CELL_MASS, TCUR,
    STOP 1
 END IF
 
+! SET MAX ORDER
+MAXORD_C = 5
+IF (IS_EXPONENT_LT_1) MAXORD_C = 1
+IERR_C = FCVODESETMAXORD(CVODE_MEM, MAXORD_C)
+IF (IERR_C /= 0) THEN
+   WRITE(LU_ERR,*) 'ERROR IN FCVODESETMAXORD, IERR = ', IERR_C, '; HALTING'
+   STOP 1
+END IF
+
 ! SET ERROR HANDLER
 IERR_C = FCVODESETERRHANDLERFN(CVODE_MEM, C_FUNLOC(FDS_CVODE_ERR_HANDLER), C_NULL_PTR)
 IF (IERR_C /= 0) THEN
@@ -920,7 +962,8 @@ SUBROUTINE CVODE_SERIAL(CC,ZZ_0, TMP_IN, PR_IN, ZETA0, TAU_MIX, CELL_MASS, TCUR,
    ONLY_FIRST_STEP = .TRUE.
    IF (WRITE_SUBSTEPS) THEN ! This WRITE_SUBSTEPS is only true for few verification cases.
       ONLY_FIRST_STEP = .FALSE.
-      ALLOCATE(CVODE_SUBSTEP_DATA((CVODE_MAX_TRY+1)*MAX_CVODE_SUBSTEPS, N_TRACKED_SPECIES+4))
+      IF (.NOT. ALLOCATED(CVODE_SUBSTEP_DATA)) &
+          ALLOCATE(CVODE_SUBSTEP_DATA((CVODE_MAX_TRY+1)*MAX_CVODE_SUBSTEPS, N_TRACKED_SPECIES+4))
    ENDIF
 
    SUBSTEP_COUNT = 0
@@ -941,11 +984,7 @@ SUBROUTINE CVODE_SERIAL(CC,ZZ_0, TMP_IN, PR_IN, ZETA0, TAU_MIX, CELL_MASS, TCUR,
       ENDIF  
    END DO
 
-   IF (WRITE_SUBSTEPS) THEN
-      TOTAL_SUBSTEPS_TAKEN = SUBSTEP_COUNT
-      STOP_STATUS=CVODE_SUBSTEP_STOP
-      RETURN
-   ENDIF   
+
 ENDIF
 
 IF (IERR_C /= 0) THEN
@@ -999,6 +1038,12 @@ SUBROUTINE CVODE_SERIAL(CC,ZZ_0, TMP_IN, PR_IN, ZETA0, TAU_MIX, CELL_MASS, TCUR,
 CALL FN_VDESTROY(SUNATOL)
 IERR_C = FSUNCONTEXT_FREE(SUNCTX)
 
+IF (WRITE_SUBSTEPS) THEN
+   TOTAL_SUBSTEPS_TAKEN = SUBSTEP_COUNT
+   STOP_STATUS=CVODE_SUBSTEP_STOP
+   RETURN
+ENDIF
+
 
 END SUBROUTINE CVODE_SERIAL
 

Source/cons.f90

@@ -200,6 +200,7 @@ MODULE GLOBAL_CONSTANTS
 LOGICAL :: WRITE_XYZ=.FALSE.                !< Indicates that a Plot3D geometry file is specified by user
 LOGICAL :: WRITE_STL=.FALSE.                !< Indicates that a STL geometry file is specified by user
 LOGICAL :: CHECK_POISSON=.FALSE.            !< Check the accuracy of the Poisson solver
+LOGICAL :: WRITE_PARCSRPCG_MATRIX=.FALSE.   !< If true, write out matrix for UGLMAT HYPRE solver
 LOGICAL :: TWO_D=.FALSE.                    !< Perform a 2-D simulation
 LOGICAL :: SETUP_ONLY=.FALSE.               !< Indicates that the calculation should be stopped before time-stepping
 LOGICAL :: CHECK_MESH_ALIGNMENT=.FALSE.     !< Indicates that the user wants to check the mesh alignment and then stop
@@ -587,8 +588,8 @@ MODULE GLOBAL_CONSTANTS
 ! Logical units and output file names
 
 INTEGER                              :: LU_ERR=ERROR_UNIT,LU_END=2,LU_GIT=3,LU_SMV=4,LU_INPUT=5,LU_OUTPUT=6,LU_STOP=7,LU_CPU=8,&
-                                        LU_CATF=9,LU_RDIR=10,LU_GDIR=11,LU_SETCC=12,LU_BINGEOM=13,LU_PARAVIEW=14,LU_STL=15,&
-                                        LU_VRDIR=16,LU_WDIR=17
+                                        LU_CATF=9,LU_RDIR=10,LU_GDIR=11,LU_SETCC=12,LU_BINGEOM=13,LU_PARCSRPCG_MATRIX=14, &
+                                        LU_PARAVIEW=15,LU_STL=16,LU_VRDIR=17,LU_WDIR=18
 INTEGER                              :: LU_MASS,LU_HRR,LU_STEPS,LU_NOTREADY,LU_VELOCITY_ERROR,LU_CFL,LU_LINE=-1,LU_CUTCELL, &
                                         LU_CVODE_SUBSTEPS
 INTEGER                              :: LU_HISTOGRAM,LU_HVAC
@@ -949,6 +950,7 @@ MODULE CHEMCONS
 INTEGER  :: MAX_CVODE_SUBSTEPS=100000
 REAL(EB) :: MAX_CHEM_TIME=1.E-6_EB
 INTEGER  :: CVODE_MAX_TRY=4
+LOGICAL  :: IS_EXPONENT_LT_1 = .FALSE.
 
 ! FOR WRITING CVODE SUBSTEPS
 LOGICAL  :: WRITE_CVODE_SUBSTEPS = .FALSE.

Source/devc.f90

@@ -46,7 +46,6 @@ MODULE DEVICE_VARIABLES
    INTEGER :: I1=-1,I2=-1,J1=-1,J2=-1,K1=-1,K2=-1
    !> !\}
    INTEGER :: N_PATH=0 !< Number of grid cells along subdevice path for TRANSMISSION or PATH OBSCURATION
-   INTEGER :: N_VALUES=0 !< Number of values for the subdevice used for computing spatial statistics
    !> !\{
    !> Grid index for a grid cell along subdevice path for TRANSMISSION or PATH OBSCURATION
    INTEGER, ALLOCATABLE, DIMENSION(:) :: I_PATH,J_PATH,K_PATH