From 46a7e25bf79bef833a5b960e1f6160e585313bcc Mon Sep 17 00:00:00 2001
From: Cheng Li <69489965+chengcli@users.noreply.github.com>
Date: Sun, 13 Oct 2024 13:39:37 -0400
Subject: [PATCH] fix bugs in netcdf and new_blockdt (#181)

- fix new_blockdt
- fix 3d netcdf output
---
 patches/21.new_blockdt.patch | 14 +++++++++++---
 src/outputs/netcdf.cpp       |  2 +-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/patches/21.new_blockdt.patch b/patches/21.new_blockdt.patch
index 94a10ae1..f09570d2 100644
--- a/patches/21.new_blockdt.patch
+++ b/patches/21.new_blockdt.patch
@@ -1,11 +1,11 @@
 diff --git a/src/hydro/new_blockdt.cpp b/src/hydro/new_blockdt.cpp
-index 0dfe3b29..71e4f7aa 100644
+index c664de5d..9286f0d7 100644
 --- a/src/hydro/new_blockdt.cpp
 +++ b/src/hydro/new_blockdt.cpp
 @@ -29,6 +29,10 @@
  #include "hydro.hpp"
  #include "hydro_diffusion/hydro_diffusion.hpp"
-
+ 
 +// snap injection
 +#include <impl.hpp>
 +#include <snap/implicit/implicit_solver.hpp>
@@ -13,7 +13,15 @@ index 0dfe3b29..71e4f7aa 100644
  // MPI/OpenMP header
  #ifdef MPI_PARALLEL
  #include <mpi.h>
-@@ -112,9 +116,21 @@ void Hydro::NewBlockTimeStep() {
+@@ -82,6 +86,7 @@ void Hydro::NewBlockTimeStep() {
+ #pragma ivdep
+         for (int i=is; i<=ie; ++i) {
+           wi[IDN] = w(IDN,k,j,i);
++          for (int n=1; n<IVX; ++n) wi[n] = w(n,k,j,i);
+           wi[IVX] = w(IVX,k,j,i);
+           wi[IVY] = w(IVY,k,j,i);
+           wi[IVZ] = w(IVZ,k,j,i);
+@@ -115,9 +120,21 @@ void Hydro::NewBlockTimeStep() {
                Real speed1 = std::max(cspeed, (std::abs(wi[IVX]) + cs));
                Real speed2 = std::max(cspeed, (std::abs(wi[IVY]) + cs));
                Real speed3 = std::max(cspeed, (std::abs(wi[IVZ]) + cs));
diff --git a/src/outputs/netcdf.cpp b/src/outputs/netcdf.cpp
index 78a4645d..390e2e62 100644
--- a/src/outputs/netcdf.cpp
+++ b/src/outputs/netcdf.cpp
@@ -360,7 +360,7 @@ void NetcdfOutput::WriteOutputFile(Mesh *pm, ParameterInput *pin, bool flag) {
 
     if (ncells3 > 1) {
       for (int k = out_ks; k <= out_ke + 1; ++k)
-        data[k - out_ks] = (float)(pmb->pcoord->x1f(k));
+        data[k - out_ks] = (float)(pmb->pcoord->x3f(k));
       nc_put_var_float(ifile, ivx3f, data);
     }