Code keeps filling up my computer! I've implemented a compressed binary output transiant output

fd9034 · fd9034 · commit a1137b5ee630 · 2026-01-15T13:18:42.000Z
Added a new input flag _CompressedOutput to param.in to enable binary 'stream' output in mod_output.f90. Also added a USER_MANUAL.md to docs/.
diff --git a/docs/USER_MANUAL.md b/docs/USER_MANUAL.md
@@ -0,0 +1,140 @@
+# HeatFlow User Manual
+
+This manual provides a concise guide to configuring and running simulations using the **HeatFlow** software. The software simulates heat transport using finite difference methods, primarily focusing on the Cattaneo (hyperbolic heat equation) and Fourier models.
+
+## Input Files
+
+The simulation is controlled by three main input files located in the `inputs/` directory:
+1.  **`param.in`**: Simulation parameters (time steps, flags, boundary conditions).
+2.  **`mat.in`**: Material properties.
+3.  **`system.in`**: Geometry and grid definition.
+
+### 1. `param.in` (Simulation Parameters)
+
+This file uses a `KEYWORD = VALUE` format. Comments can be added using `!`.
+
+#### General Settings
+| Keyword | Type | Default | Description |
+| :--- | :--- | :--- | :--- |
+| `_RunName` | String | `default` | Name of the simulation run. |
+| `IVERB` | Integer | `1` | Verbosity level (higher = more output). |
+| `ntime` | Integer | `10` | Total number of time steps. |
+| `time_step` | Double | `1.0` | Time step size. |
+| `freq` | Double | `1.0` | Frequency of the heater. |
+| `icattaneo` | Integer | `1` | Switch for Cattaneo term (`1` = On, `0` = Off/Fourier). |
+| `isteady` | Integer | `0` | Steady state switch (`1` = Steady state, `0` = Transient). |
+| `heattime` | Integer | `0` | Number of steps for which heating is applied (case 2). |
+| `TempDepProp`| Integer | `0` | Flag for temperature dependent properties. |
+
+#### Boundary & Conditions
+| Keyword | Type | Default | Description |
+| :--- | :--- | :--- | :--- |
+| `iboundary` | Integer | `1` | Boundary condition type. |
+| `Periodic` | String | `''` | Periodic boundaries. Contains 'x', 'y', or 'z' (e.g., `'xy'`). |
+| `kappaBound` | Double | `0.0` | Global boundary thermal conductivity (sets all planes). |
+| `kappaBoundx1`...`z2` | Double | `0.0` | Specific boundary conductivity (e.g., `kappaBoundx1` for x=1 plane). |
+| `T_System` | Double | `300.0` | Initial system temperature. |
+| `T_Bath` | Double | - | Global bath temperature (sets all boundaries boundaries). |
+| `T_Bathx1`...`z2` | Double | `T_Bath` | Specific boundary temperatures. |
+| `T_BathCG` | Double | `0.0` | Constant gradient bath temperature. |
+| `CG_dir` | String | `' '` | Direction for constant gradient (e.g., `'+x'`, `'-y'`). |
+| `T_BathCC` | Logical| `F` | Scale constant gradient with DeltaT. |
+| `BR` | Double | `1.0` | Bath Ratio (scaling factor). |
+
+#### Power
+| Keyword | Type | Default | Description |
+| :--- | :--- | :--- | :--- |
+| `power_in` | Double | `0.0` | Power input for the heater. |
+
+#### Flags (Logical)
+All flags default to `.False.`. Set to `.True.` (or `T`) to enable.
+- `_Check_Sparse_Full`: Check if simulation is sparse or full.
+- `_Check_Stability`: Perform stability check.
+- `_Check_Steady_State`: Check for steady state convergence.
+- `_WriteToTxt`: Enable writing output to text files.
+- `_Percentage_Completion`: Show progress % in output.
+- `_Test_Run`: Flag for test runs.
+- `_InputTempDis`: Load initial temperature distribution from file.
+- `_FullRestart`: Perform a full restart.
+
+#### Output Control
+Defines the region of the grid to write to output.
+| Keyword | Type | Default | Description |
+| :--- | :--- | :--- | :--- |
+| `write_every` | Integer | `1` | Write output every N steps. |
+| `start_ix`, `end_ix` | Integer | `1`..`Nx` | X-range for output. |
+| `start_iy`, `end_iy` | Integer | `1`..`Ny` | Y-range for output. |
+| `start_iz`, `end_iz` | Integer | `1`..`Nz` | Z-range for output. |
+
+---
+
+### 2. `mat.in` (Material Properties)
+
+Defines the physical properties for each material index used in the system. The file ends with a line containing `0`.
+
+**Format:**
+```
+<Material_Index>
+keyword = value
+...
+0
+```
+
+| Keyword | Description |
+| :--- | :--- |
+| `heat_capacity` | Specific heat capacity. |
+| `kappa` | Thermal conductivity. |
+| `rho` | Density. |
+| `tau` | Relaxation time (for Cattaneo). |
+| `em` | Emissivity / Parameter (usage depends on physics context). |
+| `vel` | Velocity vector (3 components, e.g., `vel = 1.0 0.0 0.0`). |
+
+**Example:**
+```
+1
+heat_capacity = 4200
+kappa = 0.541
+rho = 997
+tau = 1e-12
+vel = 0.0 0.0 0.0
+0
+```
+
+---
+
+### 3. `system.in` (Geometry/Mesh)
+
+Defines the simulation grid and the material distribution.
+
+**Structure:**
+1.  **Grid Dimensions**: `nx ny nz`
+2.  **Physical Dimensions**: `Lx Ly Lz`
+3.  **Grid Data**: A list of `MaterialID:HeaterID` for every cell.
+
+The file is read in the order: Z-planes, then Y-rows, then X-columns.
+Each line in the file (after header) corresponds to one row (X-direction).
+
+**Example:**
+```
+10 10 1
+0.01 0.01 0.001
+
+! Z=1, Y=1 Row
+1:0 1:0 1:0 1:0 1:0 1:0 1:0 1:0 1:0 1:0
+! Z=1, Y=2 Row
+1:0 1:0 ...
+```
+- `1:0` means Material ID 1, Heater ID 0 (no heater).
+- `1:1` means Material ID 1, Heater ID 1 (active heater).
+
+## Execution
+
+Ensure the `inputs/` directory exists with the three required files. Run the executable from the directory containing `inputs/`.
+
+```bash
+./ThermalFlow.x
+```
+or via `fpm`:
+```bash
+fpm run --profile release
+```
diff --git a/src/heatflow/mod_inputs.f90 b/src/heatflow/mod_inputs.f90
@@ -91,7 +91,7 @@ module inputs
   integer(int12) :: start_ix, end_ix, start_iy, end_iy, start_iz, end_iz, TempDepProp, heated_steps
   ! flags
   logical :: Check_Sparse_Full, Check_Stability, Check_Steady_State
-  logical :: WriteToTxt, LPercentage, InputTempDis
+  logical :: WriteToTxt, LPercentage, InputTempDis, CompressedOutput
   logical ::  Test_Run = .FALSE., FullRestart = .FALSE.
 
   ! Name of simiulation run
@@ -204,7 +204,7 @@ end subroutine read_all_files
   subroutine read_param(unit)
     implicit none
     integer:: unit, Reason
-    integer,dimension(45)::readvar
+    integer,dimension(46)::readvar
     character(1024)::buffer
 
     readvar(:)=0
@@ -221,6 +221,7 @@ subroutine read_param(unit)
     RunName = 'default'
     RunName = trim(adjustl(RunName))
     WriteToTxt = .FALSE.
+    CompressedOutput = .FALSE.
     ntime = 10
     heated_steps = 0
     write_every = 1
@@ -325,6 +326,7 @@ subroutine read_param(unit)
        CALL assignD(buffer,"BR",BR,readvar(43))
        CALL assignL(buffer,"T_BathCC",T_BathCC,readvar(44))
        CALL assignS(buffer,"CG_dir",CG_dir,readvar(45))
+       CALL assignL(buffer,"_CompressedOutput",CompressedOutput,readvar(46))
        !^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
     end do
@@ -520,6 +522,10 @@ subroutine check_param(readvar,n)
        readvar(39) = 1
     end if
 
+    if (readvar(46) .eq. 0) then
+       readvar(46) = 1
+    end if
+
     if (any(readvar.eq.0)) then
        write(6,*)
        write(6,'(A43)') '###############################'
@@ -554,6 +560,7 @@ subroutine check_param(readvar,n)
        write(6,'(A35,L1)')      '  _FullRestart       = ', FullRestart
        write(6,'(A35,A)')       '  _RunName           = ', trim(RunName)
        write(6,'(A35,L1)')      '  _WriteToTxt        = ', WriteToTxt
+       write(6,'(A35,L1)')      '  _CompressedOutput  = ', CompressedOutput
        write(6,'(A35,I12)')     '   ntime       = ', ntime
        write(6,'(A35,I12)')     '   heattime    = ', heated_steps
        write(6,'(A35,I12)')     '   write_every = ', write_every
diff --git a/src/heatflow/mod_output.f90 b/src/heatflow/mod_output.f90
@@ -44,7 +44,7 @@
 module output
   use constants, only: real12, int12, TINY, fields
   use inputs, only: nx,ny,nz, time_step, grid, NA, Check_Steady_State, ntime, WriteToTxt
-  use inputs, only: Test_Run, freq, RunName, FullRestart, IVERB, write_every
+  use inputs, only: Test_Run, freq, RunName, FullRestart, IVERB, write_every, CompressedOutput
   use inputs, only: start_ix, end_ix, start_iy, end_iy, start_iz, end_iz
   use globe_data, only: Temp_p,Temp_pp, heat, heated_volume, logname
   implicit none
@@ -92,11 +92,17 @@ subroutine data_write(itime)
           ! find most recent log file and open it
           !---------------------------------------
           CALL last_log(logname,outdir)
-          open(logunit,file=logname)
-         !  print*, logunit
-         !  print*, logname
-          write(logunit,*) real((itime-1)*(time_step)), &
-               (Temp_cur(start_ix:end_ix, start_iy:end_iy, start_iz:end_iz))
+          if (CompressedOutput) then
+             open(logunit,file=logname, status='unknown', access='stream', position='append')
+             write(logunit) real((itime-1)*(time_step), kind=real12)
+             write(logunit) (Temp_cur(start_ix:end_ix, start_iy:end_iy, start_iz:end_iz))
+          else
+             open(logunit,file=logname)
+            !  print*, logunit
+            !  print*, logname
+             write(logunit,*) real((itime-1)*(time_step)), &
+                  (Temp_cur(start_ix:end_ix, start_iy:end_iy, start_iz:end_iz))
+          end if
           close(logunit)
           !^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        end if
@@ -110,17 +116,23 @@ subroutine data_write(itime)
     ! write out to log file
     !---------------------------------------
     if (.not. Test_run) then
-      if (WriteToTxt) then
-         if (mod(itime, write_every) .eq. 0) then
-            write(*, *) 'Writing Temperature difference to file'
-            ! print*, logunit
-            ! print*, logname
-            open(logunit,file=logname, status='old', position='append')
-            write(logunit,*) real((itime-1)*(time_step)), &
-               (Temp_cur(start_ix:end_ix, start_iy:end_iy, start_iz:end_iz))
-            close(logunit)
-         end if
-      endif
+       if (mod(itime, write_every) .eq. 0) then
+          if (CompressedOutput) then
+             write(*, *) 'Writing Temperature (Compressed) to file'
+             open(logunit,file=logname, status='unknown', access='stream', position='append')
+             write(logunit) real((itime-1)*(time_step), kind=real12)
+             write(logunit) (Temp_cur(start_ix:end_ix, start_iy:end_iy, start_iz:end_iz))
+             close(logunit)
+          elseif (WriteToTxt) then
+             write(*, *) 'Writing Temperature difference to file'
+             ! print*, logunit
+             ! print*, logname
+             open(logunit,file=logname, status='old', position='append')
+             write(logunit,*) real((itime-1)*(time_step)), &
+                (Temp_cur(start_ix:end_ix, start_iy:end_iy, start_iz:end_iz))
+             close(logunit)
+          end if
+       end if
     end if
     !^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -202,8 +214,13 @@ subroutine last_log(logname,outdir)
    i = 0
    flag=.true.
    do while (flag)
-      write(logname, '(A,A,I2.2)') trim(adjustl(outdir)) // 'output_' // &
-           trim(adjustl(RunName)),'_',  i
+      if (CompressedOutput) then
+         write(logname, '(A,A,I2.2,A)') trim(adjustl(outdir)) // 'output_' // &
+              trim(adjustl(RunName)),'_',  i, '.bin'
+      else
+         write(logname, '(A,A,I2.2)') trim(adjustl(outdir)) // 'output_' // &
+              trim(adjustl(RunName)),'_',  i
+      endif
       inquire(file=logname, exist=flag)
       i = i+1
    end do
diff --git a/src/heatflow/mod_petsc_solver.f90 b/src/heatflow/mod_petsc_solver.f90
@@ -12,7 +12,7 @@ module petsc_solver
   ! 'GAMG' = Algebraic Multigrid (best for elliptic PDEs, 10-20x faster)
   ! 'ILU'  = Incomplete LU (good general purpose, robust)
   ! 'LU'   = Direct solver (most robust, uses more memory)
-  character(len=10), parameter :: PRECONDITIONER = 'GAMG'  ! <-- Change here!
+  character(len=10), parameter :: PRECONDITIONER = 'ILU'  ! <-- Change here!
   ! ====================================
 
   ! Persistent PETSc objects (reused across timesteps for memory efficiency)
