Flow past cylinder LMeX Tutorial.

Docs/source/manual/LMeXControls.rst

@@ -1,6 +1,8 @@
 PeleLMeX controls
 =================
 
+.. _sec:control:
+
 The input file specified on the command line is a free-format text file, one entry per row, that specifies input data processed by the AMReX ``ParmParse`` module.
 This file needs to specified along with the executable as an `argv` option, for example:
 
@@ -76,10 +78,11 @@ IO parameters
 
     #--------------------------IO CONTROL--------------------------
     amr.plot_int         = 20              # [OPT, DEF=-1] Frequency (as step #) for writting plot file
-    amr.plot_per         = 002             # [OPT, DEF=-1] Period (time in s) for writting plot file
+    amr.plot_per         = 0.002           # [OPT, DEF=-1] Period (time in s) for writting plot file
     amr.plot_per_exact   = 1               # [OPT, DEF=0] Flag to enforce exactly plt_per by shortening dt
     amr.plot_file        = "plt_"          # [OPT, DEF="plt_"] Plot file prefix
     amr.check_int        = 100             # [OPT, DEF=-1] Frequency (as step #) for writting checkpoint file
+    amr.check_per        = 0.05            # [OPT, DEF=-1] Period (time in s) for writting checkpoint file
     amr.check_file       = "chk"           # [OPT, DEF="chk"] Checkpoint file prefix
     amr.file_stepDigits  = 6               # [OPT, DEF=5] Number of digits when adding nsteps to plt and chk names
     amr.derive_plot_vars = avg_pressure ...# [OPT, DEF=""] List of derived variable included in the plot files

Docs/source/manual/Tutorials.rst

@@ -7,9 +7,8 @@ Tutorials
 =========
 
 This sections includes several self-contained tutorials.
-TODO
 
 .. toctree::
    :maxdepth: 1
 
-
+   Tutorials_FlowPastCyl.rst

Exec/RegTests/EB_FlowPastCylinder/input.2d-Re500

@@ -0,0 +1,69 @@
+#----------------------DOMAIN DEFINITION-------------------------
+geometry.is_periodic = 0 1                # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = -0.02 -0.02        # x_lo y_lo (z_lo)
+geometry.prob_hi     =  0.10  0.02        # x_hi y_hi (z_hi)
+
+#--------------------------BC FLAGS------------------------------
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+peleLM.lo_bc = Inflow  Interior
+peleLM.hi_bc = Outflow Interior
+
+#-------------------------AMR CONTROL----------------------------
+amr.n_cell          = 192 64           # Level 0 number of cells in each direction
+amr.v               = 1                # AMR verbose
+amr.max_level       = 0                # maximum level number allowed
+amr.ref_ratio       = 2 2 2 2          # refinement ratio
+amr.regrid_int      = 5                # how often to regrid
+amr.n_error_buf     = 2 2 2 2          # number of buffer cells in error est
+amr.grid_eff        = 0.7              # what constitutes an efficient grid
+amr.blocking_factor = 16               # block factor in grid generation (min box size)
+amr.max_grid_size   = 64               # max box size
+
+#--------------------------- Problem ----------------------------
+prob.T_mean = 300.0
+prob.P_mean = 101325.0
+prob.meanFlowMag = 4.255
+prob.meanFlowDir = 1
+
+#-----------------INPUTS TO CONSTANT TRANSPORT ------------------
+transport.units                  = MKS
+transport.const_viscosity        = 0.0001
+transport.const_bulk_viscosity   = 0.0
+transport.const_conductivity     = 0.0
+transport.const_diffusivity      = 0.0
+
+#---------------------------TIME STEPPING------------------------
+amr.max_step = 30000
+amr.stop_time = 0.025
+amr.dt_shrink = 0.1
+amr.dt_change_max = 1.1
+amr.cfl = 0.7
+
+#-------------------------PELELMEX CONTROLS----------------------
+peleLM.v = 1
+
+#---------------------------IO CONTROL---------------------------
+#amr.restart = chk_07136
+amr.check_file = "chk_"
+amr.check_per = 0.05
+amr.plot_file = "plt_"
+amr.plot_per = 0.005
+amr.derive_plot_vars = avg_pressure mag_vort
+
+#------------------------- EB SETUP -----------------------------
+eb2.geom_type = sphere
+eb2.sphere_radius = 0.005
+eb2.sphere_center = 0.0 0.0
+eb2.sphere_has_fluid_inside = 0
+eb2.small_volfrac = 1.0e-4
+
+#--------------------REFINEMENT CONTROL--------------------------
+amr.refinement_indicators = VortL VortH
+amr.VortL.max_level     = 1
+amr.VortL.value_less    = -1000
+amr.VortL.field_name    = mag_vort
+amr.VortH.max_level     = 1
+amr.VortH.value_greater = 1000
+amr.VortH.field_name    = mag_vort

Exec/RegTests/FlameSheet/GNUmakefile

@@ -13,7 +13,7 @@ VERBOSE         = FALSE
 TINY_PROFILE    = FALSE
 
 # Compilation
-COMP            = gnu
+COMP            = llvm
 USE_MPI         = TRUE
 USE_OMP         = FALSE
 USE_CUDA        = FALSE

Exec/RegTests/FlameSheet/input.2d-regt

@@ -20,7 +20,7 @@ amr.regrid_int      = 5                # how often to regrid
 amr.n_error_buf     = 1 1 2 2          # number of buffer cells in error est
 amr.grid_eff        = 0.7              # what constitutes an efficient grid
 amr.blocking_factor = 16               # block factor in grid generation (min box size)
-amr.max_grid_size   = 64               # max box size
+amr.max_grid_size   = 256               # max box size
 
 
 #--------------------------- Problem -------------------------------

README.md

@@ -6,7 +6,7 @@
 
 ## Overview
 
-*PeleLMeX* is a non-subcycling version of [*PeleLM*](https://github.com/AMReX-Combustion/PeleLM) based on AMReX's [AmrCore](https://amrex-codes.github.io/amrex/docs_html/AmrCore.html) and borrowing from the incompressible solver [incflo](https://github.com/AMReX-Codes/incflo). 
+*PeleLMeX* is a non-subcycling version of [*PeleLM*](https://github.com/AMReX-Combustion/PeleLM) based on AMReX's [AmrCore](https://amrex-codes.github.io/amrex/docs_html/AmrCore.html) and borrowing from the incompressible solver [incflo](https://github.com/AMReX-Codes/incflo).
 
 *PeleLMeX* is part of the [Pele combustion Suite](https://amrex-combustion.github.io/).
 
@@ -28,11 +28,13 @@ https://amrex-combustion.github.io/PeleLMeX/manual/html/Model.html#pelelmex-algo
 
 A set of self-contained tutorials describing more complex problems is also provided:
 
+https://amrex-combustion.github.io/PeleLMeX/manual/html/Tutorials.html
+
 ## Installation
 
 ### Using git submodules
 
-You can clone the PeleLMeX and tested versions of its submodules 
+You can clone the PeleLMeX and tested versions of its submodules
 ([amrex](https://github.com/AMReX-Codes/amrex), [AMReX-Hydro](https://github.com/AMReX-Codes/AMReX-Hydro) and [PelePhysics](https://github.com/AMReX-Combustion/PelePhysics)) using:
 
 ```
@@ -91,14 +93,14 @@ To clean the installation, use either `make clean` or `make realclean`.
 
 ## Contributing
 
-New contributions to *PeleLM* are welcome ! Contributing Guidelines are provided in [CONTRIBUTING.md](CONTRIBUTING.md).
+New contributions to *PeleLMeX* are welcome ! Contributing Guidelines are provided in [CONTRIBUTING.md](CONTRIBUTING.md).
 
 ## Acknowledgment
 
 This research was supported by the Exascale Computing Project (ECP), Project
-Number: 17-SC-20-SC, a collaborative effort of two DOE organizations -- the 
+Number: 17-SC-20-SC, a collaborative effort of two DOE organizations -- the
 Office of Science and the National Nuclear Security Administration --
 responsible for the planning and preparation of a capable exascale ecosystem --
-including software, applications, hardware, advanced system engineering, and 
+including software, applications, hardware, advanced system engineering, and
 early testbed platforms -- to support the nation's exascale computing
 imperative.

Source/PeleLM.H

@@ -1095,6 +1095,7 @@ class PeleLM : public amrex::AmrCore {
    amrex::Real m_plot_per_approx = -1.;
    amrex::Real m_plot_per_exact = -1.;
    int m_check_int = 0;
+   amrex::Real m_check_per = -1.;
    int m_message_int = 10;
    int m_evaluatePlotVarCount = 0;
    int m_plot_grad_p = 1;

Source/PeleLMEvolve.cpp

@@ -153,8 +153,34 @@ PeleLM::writeCheckNow()
 
    if ( m_check_int > 0 && (m_nstep % m_check_int == 0) ) {
       write_now = true;
+   } else if (m_check_per > 0.0) {
+      // Check to see if we've crossed a plot_per interval by comparing
+      // the number of intervals that have elapsed for both the current
+      // time and the time at the beginning of this timestep.
+      int num_per_old = static_cast<int>((m_cur_time-m_dt) / m_check_per);
+      int num_per_new = static_cast<int>((m_cur_time     ) / m_check_per);
+      // Before using these, however, we must test for the case where we're
+      // within machine epsilon of the next interval. In that case, increment
+      // the counter, because we have indeed reached the next plot_per interval
+      // at this point.
+      const Real eps = std::numeric_limits<Real>::epsilon() * 10.0_rt * std::abs(m_cur_time);
+      const Real next_check_time = (num_per_old + 1) * m_check_per;
+      if ((num_per_new == num_per_old) && std::abs(m_cur_time - next_check_time) <= eps)
+      {
+         num_per_new += 1;
+      }
+      // Similarly, we have to account for the case where the old time is within
+      // machine epsilon of the beginning of this interval, so that we don't double
+      // count that time threshold -- we already plotted at that time on the last timestep.
+      if ((num_per_new != num_per_old) && std::abs((m_cur_time - m_dt) - next_check_time) <= eps)
+      {
+         num_per_old += 1;
+      }
+      if (num_per_old != num_per_new)
+      {
+         write_now = true;
+      }
    }
-   // TODO : time controled ?
 
    return write_now;
 }

Source/PeleLMInit.cpp

@@ -297,7 +297,7 @@ void PeleLM::initData() {
       if (m_plot_int > 0 || m_plot_per_approx > 0. || m_plot_per_exact > 0.) {
          WritePlotFile();
       }
-      if (m_check_int > 0 ) {
+      if (m_check_int > 0 || m_check_per > 0.) {
          WriteCheckPointFile();
       }
 

Source/PeleLMSetup.cpp

@@ -530,6 +530,7 @@ void PeleLM::readIOParameters() {
 
    pp.query("check_file", m_check_file);
    pp.query("check_int" , m_check_int);
+   pp.query("check_per" , m_check_per);
    pp.query("restart" , m_restart_chkfile);
    pp.query("initDataPlt" , m_restart_pltfile);
    pp.query("initDataPltSource" , pltfileSource);