diff --git a/CMake/BuildREMORAExe.cmake b/CMake/BuildREMORAExe.cmake
index 8cda84a2..fc5cd323 100644
--- a/CMake/BuildREMORAExe.cmake
+++ b/CMake/BuildREMORAExe.cmake
@@ -15,11 +15,6 @@ function(build_remora_lib remora_lib_name)
   include(${CMAKE_SOURCE_DIR}/CMake/SetREMORACompileFlags.cmake)
   set_remora_compile_flags(${remora_lib_name})
 
-  set(REMORA_EOS_DIR "${CMAKE_SOURCE_DIR}/Source")
-  target_sources(${remora_lib_name} PRIVATE
-                 ${REMORA_EOS_DIR}/EOS.H)
-  target_include_directories(${remora_lib_name} SYSTEM PUBLIC ${REMORA_EOS_DIR})
-
   if(REMORA_ENABLE_PARTICLES)
     target_sources(${remora_lib_name} PRIVATE
                    ${SRC_DIR}/Particles/REMORA_PC_Evolve.cpp
@@ -32,15 +27,15 @@ function(build_remora_lib remora_lib_name)
 
   if(REMORA_ENABLE_PNETCDF)
     target_sources(${remora_lib_name} PRIVATE
-                   ${SRC_DIR}/IO/NCInterface.H
-                   ${SRC_DIR}/IO/NCPlotFile.H
-                   ${SRC_DIR}/IO/NCFile.H
-                   ${SRC_DIR}/IO/NCInterface.cpp
-                   ${SRC_DIR}/IO/NCPlotFile.cpp
-                   ${SRC_DIR}/IO/NCFile.cpp
-                   ${SRC_DIR}/IO/ReadFromInitNetcdf.cpp
-                   ${SRC_DIR}/IO/ReadFromBdryNetcdf.cpp
-                   ${SRC_DIR}/BoundaryConditions/BoundaryConditions_netcdf.cpp
+                   ${SRC_DIR}/IO/REMORA_NCInterface.H
+                   ${SRC_DIR}/IO/REMORA_NCPlotFile.H
+                   ${SRC_DIR}/IO/REMORA_NCFile.H
+                   ${SRC_DIR}/IO/REMORA_NCInterface.cpp
+                   ${SRC_DIR}/IO/REMORA_NCPlotFile.cpp
+                   ${SRC_DIR}/IO/REMORA_NCFile.cpp
+                   ${SRC_DIR}/IO/REMORA_ReadFromInitNetcdf.cpp
+                   ${SRC_DIR}/IO/REMORA_ReadFromBdryNetcdf.cpp
+                   ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp
                    ${SRC_DIR}/Initialization/REMORA_init_from_netcdf.cpp)
     target_compile_definitions(${remora_lib_name} PUBLIC REMORA_USE_NETCDF)
   endif()
@@ -51,14 +46,14 @@ function(build_remora_lib remora_lib_name)
 
   target_sources(${remora_lib_name}
      PRIVATE
-       ${SRC_DIR}/Derive.cpp
+       ${SRC_DIR}/REMORA_Derive.cpp
        ${SRC_DIR}/REMORA.cpp
        ${SRC_DIR}/REMORA_SumIQ.cpp
        ${SRC_DIR}/REMORA_Tagging.cpp
-       ${SRC_DIR}/BoundaryConditions/BoundaryConditions_cons.cpp
-       ${SRC_DIR}/BoundaryConditions/BoundaryConditions_xvel.cpp
-       ${SRC_DIR}/BoundaryConditions/BoundaryConditions_yvel.cpp
-       ${SRC_DIR}/BoundaryConditions/BoundaryConditions_zvel.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp
        ${SRC_DIR}/BoundaryConditions/REMORA_FillPatch.cpp
        ${SRC_DIR}/BoundaryConditions/REMORA_FillPatcher.cpp
        ${SRC_DIR}/BoundaryConditions/REMORA_PhysBCFunct.cpp
@@ -66,10 +61,10 @@ function(build_remora_lib remora_lib_name)
        ${SRC_DIR}/Initialization/REMORA_init1d.cpp
        ${SRC_DIR}/Initialization/REMORA_init_bcs.cpp
        ${SRC_DIR}/Initialization/REMORA_make_new_level.cpp
-       ${SRC_DIR}/IO/Checkpoint.cpp
-       ${SRC_DIR}/IO/Plotfile.cpp
-       ${SRC_DIR}/IO/writeJobInfo.cpp
-       ${SRC_DIR}/IO/console_io.cpp
+       ${SRC_DIR}/IO/REMORA_Checkpoint.cpp
+       ${SRC_DIR}/IO/REMORA_Plotfile.cpp
+       ${SRC_DIR}/IO/REMORA_writeJobInfo.cpp
+       ${SRC_DIR}/IO/REMORA_console_io.cpp
        ${SRC_DIR}/TimeIntegration/REMORA_Advance.cpp
        ${SRC_DIR}/TimeIntegration/REMORA_advance_2d.cpp
        ${SRC_DIR}/TimeIntegration/REMORA_advance_2d_onestep.cpp
diff --git a/CMake/SetAmrexOptions.cmake b/CMake/SetAmrexOptions.cmake
index 0f133e72..7fd61e88 100644
--- a/CMake/SetAmrexOptions.cmake
+++ b/CMake/SetAmrexOptions.cmake
@@ -6,7 +6,7 @@ set(AMReX_MPI ${REMORA_ENABLE_MPI})
 set(AMReX_OMP ${REMORA_ENABLE_OPENMP})
 set(AMReX_PRECISION "${REMORA_PRECISION}" CACHE STRING "Floating point precision" FORCE)
 set(AMReX_EB OFF)
-set(AMReX_FORTRAN_INTREMORAACES OFF)
+set(AMReX_FORTRAN_INTERFACES OFF)
 set(AMReX_LINEAR_SOLVERS OFF)
 set(AMReX_AMRDATA OFF)
 set(AMReX_PARTICLES OFF)
diff --git a/Exec/Advection/prob.cpp b/Exec/Advection/prob.cpp
index b90b4db8..711eed20 100644
--- a/Exec/Advection/prob.cpp
+++ b/Exec/Advection/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/Channel_Test/prob.cpp b/Exec/Channel_Test/prob.cpp
index dbae5990..4540ba67 100644
--- a/Exec/Channel_Test/prob.cpp
+++ b/Exec/Channel_Test/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/DoubleGyre/prob.cpp b/Exec/DoubleGyre/prob.cpp
index 02aa8af4..e8b56eed 100644
--- a/Exec/DoubleGyre/prob.cpp
+++ b/Exec/DoubleGyre/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/DoublyPeriodic/prob.cpp b/Exec/DoublyPeriodic/prob.cpp
index 34c472ff..1c8bd2b6 100644
--- a/Exec/DoublyPeriodic/prob.cpp
+++ b/Exec/DoublyPeriodic/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/IdealMiniGrid/prob.cpp b/Exec/IdealMiniGrid/prob.cpp
index 091e9125..7a9adb59 100644
--- a/Exec/IdealMiniGrid/prob.cpp
+++ b/Exec/IdealMiniGrid/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/OCCAMS/prob.cpp b/Exec/OCCAMS/prob.cpp
index a00c1db3..fdd7eed7 100644
--- a/Exec/OCCAMS/prob.cpp
+++ b/Exec/OCCAMS/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/ParticlesOverSeaMount/prob.cpp b/Exec/ParticlesOverSeaMount/prob.cpp
index 65096fc6..297b934e 100644
--- a/Exec/ParticlesOverSeaMount/prob.cpp
+++ b/Exec/ParticlesOverSeaMount/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/Seamount/prob.cpp b/Exec/Seamount/prob.cpp
index f914243a..8b7bb39c 100644
--- a/Exec/Seamount/prob.cpp
+++ b/Exec/Seamount/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/Upwelling/prob.cpp b/Exec/Upwelling/prob.cpp
index fb63bf7a..320bfced 100644
--- a/Exec/Upwelling/prob.cpp
+++ b/Exec/Upwelling/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Exec/Upwelling_ML/prob.cpp b/Exec/Upwelling_ML/prob.cpp
index 7058ace6..c81fe125 100644
--- a/Exec/Upwelling_ML/prob.cpp
+++ b/Exec/Upwelling_ML/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 
diff --git a/Source/BoundaryConditions/Make.package b/Source/BoundaryConditions/Make.package
index 701c6ef3..51bcc6cf 100644
--- a/Source/BoundaryConditions/Make.package
+++ b/Source/BoundaryConditions/Make.package
@@ -1,10 +1,10 @@
-CEXE_sources += BoundaryConditions_xvel.cpp
-CEXE_sources += BoundaryConditions_yvel.cpp
-CEXE_sources += BoundaryConditions_zvel.cpp
-CEXE_sources += BoundaryConditions_cons.cpp
+CEXE_sources += REMORA_BoundaryConditions_xvel.cpp
+CEXE_sources += REMORA_BoundaryConditions_yvel.cpp
+CEXE_sources += REMORA_BoundaryConditions_zvel.cpp
+CEXE_sources += REMORA_BoundaryConditions_cons.cpp
 
 ifeq ($(USE_PNETCDF), TRUE)
-CEXE_sources += BoundaryConditions_netcdf.cpp
+CEXE_sources += REMORA_BoundaryConditions_netcdf.cpp
 endif
 
 CEXE_sources += REMORA_FillPatch.cpp
@@ -14,4 +14,4 @@ CEXE_sources += REMORA_PhysBCFunct.cpp
 CEXE_headers += REMORA_PhysBCFunct.H
 
 CEXE_headers += REMORA_FillPatcher.H
-CEXE_headers += TimeInterpolatedData.H
+CEXE_headers += REMORA_TimeInterpolatedData.H
diff --git a/Source/BoundaryConditions/BoundaryConditions_cons.cpp b/Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp
similarity index 100%
rename from Source/BoundaryConditions/BoundaryConditions_cons.cpp
rename to Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp
diff --git a/Source/BoundaryConditions/BoundaryConditions_netcdf.cpp b/Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp
similarity index 100%
rename from Source/BoundaryConditions/BoundaryConditions_netcdf.cpp
rename to Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp
diff --git a/Source/BoundaryConditions/BoundaryConditions_xvel.cpp b/Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp
similarity index 100%
rename from Source/BoundaryConditions/BoundaryConditions_xvel.cpp
rename to Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp
diff --git a/Source/BoundaryConditions/BoundaryConditions_yvel.cpp b/Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp
similarity index 100%
rename from Source/BoundaryConditions/BoundaryConditions_yvel.cpp
rename to Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp
diff --git a/Source/BoundaryConditions/BoundaryConditions_zvel.cpp b/Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp
similarity index 99%
rename from Source/BoundaryConditions/BoundaryConditions_zvel.cpp
rename to Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp
index 5ecc7b8e..fd42f9cc 100644
--- a/Source/BoundaryConditions/BoundaryConditions_zvel.cpp
+++ b/Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp
@@ -1,6 +1,6 @@
 #include "AMReX_PhysBCFunct.H"
 #include <REMORA_PhysBCFunct.H>
-#include <prob_common.H>
+#include <REMORA_prob_common.H>
 
 using namespace amrex;
 
diff --git a/Source/BoundaryConditions/REMORA_FillPatch.cpp b/Source/BoundaryConditions/REMORA_FillPatch.cpp
index 5aeedf08..8b5fcfa3 100644
--- a/Source/BoundaryConditions/REMORA_FillPatch.cpp
+++ b/Source/BoundaryConditions/REMORA_FillPatch.cpp
@@ -1,7 +1,7 @@
 #include <REMORA.H>
 #include <REMORA_PhysBCFunct.H>
-#include <IndexDefines.H>
-#include <TimeInterpolatedData.H>
+#include <REMORA_IndexDefines.H>
+#include <REMORA_TimeInterpolatedData.H>
 
 using namespace amrex;
 
diff --git a/Source/BoundaryConditions/REMORA_PhysBCFunct.H b/Source/BoundaryConditions/REMORA_PhysBCFunct.H
index a859be54..f5255d1f 100644
--- a/Source/BoundaryConditions/REMORA_PhysBCFunct.H
+++ b/Source/BoundaryConditions/REMORA_PhysBCFunct.H
@@ -12,9 +12,9 @@
 #include "AMReX_TypeTraits.H"
 #include "AMReX_Orientation.H"
 
-#include <TimeInterpolatedData.H>
-#include <IndexDefines.H>
-#include <DataStruct.H>
+#include <REMORA_TimeInterpolatedData.H>
+#include <REMORA_IndexDefines.H>
+#include <REMORA_DataStruct.H>
 
 using PlaneVector = amrex::Vector<amrex::FArrayBox>;
 
diff --git a/Source/BoundaryConditions/REMORA_PhysBCFunct.cpp b/Source/BoundaryConditions/REMORA_PhysBCFunct.cpp
index d45f69ff..0a45c398 100644
--- a/Source/BoundaryConditions/REMORA_PhysBCFunct.cpp
+++ b/Source/BoundaryConditions/REMORA_PhysBCFunct.cpp
@@ -1,5 +1,5 @@
 #include "AMReX_PhysBCFunct.H"
-#include "IndexDefines.H"
+#include "REMORA_IndexDefines.H"
 #include <REMORA_PhysBCFunct.H>
 
 using namespace amrex;
diff --git a/Source/BoundaryConditions/TimeInterpolatedData.H b/Source/BoundaryConditions/REMORA_TimeInterpolatedData.H
similarity index 100%
rename from Source/BoundaryConditions/TimeInterpolatedData.H
rename to Source/BoundaryConditions/REMORA_TimeInterpolatedData.H
diff --git a/Source/EOS.H b/Source/EOS.H
deleted file mode 100644
index 6c37499d..00000000
--- a/Source/EOS.H
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef _EOS_H_
-#define _EOS_H_
-
-#include <REMORA_Constants.H>
-#include <AMReX.H>
-#include <cmath>
-
-AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
-amrex::Real getTgivenRandTh(const amrex::Real rho, const amrex::Real temp)
-{
-    amrex::Real p_loc = p_0 * std::pow(R_d * temp * ip_0, Gamma);
-    return p_loc / (R_d * rho);
-}
-#endif
-
diff --git a/Source/IO/Make.package b/Source/IO/Make.package
index d4fee799..ec36a161 100644
--- a/Source/IO/Make.package
+++ b/Source/IO/Make.package
@@ -1,17 +1,17 @@
 
-CEXE_sources += Plotfile.cpp
-CEXE_sources += Checkpoint.cpp
-CEXE_sources += writeJobInfo.cpp
+CEXE_sources += REMORA_Plotfile.cpp
+CEXE_sources += REMORA_Checkpoint.cpp
+CEXE_sources += REMORA_writeJobInfo.cpp
 
-CEXE_sources += console_io.cpp
+CEXE_sources += REMORA_console_io.cpp
 
 ifeq ($(USE_PNETCDF), TRUE)
-  CEXE_sources += ReadFromInitNetcdf.cpp
-  CEXE_sources += ReadFromBdryNetcdf.cpp
-  CEXE_sources += NCInterface.cpp
-  CEXE_sources += NCPlotFile.cpp
-  CEXE_sources += NCFile.cpp
-  CEXE_headers += NCInterface.H
-  CEXE_headers += NCPlotFile.H
-  CEXE_headers += NCFile.H
+  CEXE_sources += REMORA_ReadFromInitNetcdf.cpp
+  CEXE_sources += REMORA_ReadFromBdryNetcdf.cpp
+  CEXE_sources += REMORA_NCInterface.cpp
+  CEXE_sources += REMORA_NCPlotFile.cpp
+  CEXE_sources += REMORA_NCFile.cpp
+  CEXE_headers += REMORA_NCInterface.H
+  CEXE_headers += REMORA_NCPlotFile.H
+  CEXE_headers += REMORA_NCFile.H
 endif
diff --git a/Source/IO/NCPlotFile.H b/Source/IO/NCPlotFile.H
deleted file mode 100644
index 5ce09e41..00000000
--- a/Source/IO/NCPlotFile.H
+++ /dev/null
@@ -1,4 +0,0 @@
-#ifndef _NCPLOTFILE_H_
-#define _NCPLOTFILE_H_
-extern std::string inputs_name;
-#endif
diff --git a/Source/IO/Checkpoint.cpp b/Source/IO/REMORA_Checkpoint.cpp
similarity index 100%
rename from Source/IO/Checkpoint.cpp
rename to Source/IO/REMORA_Checkpoint.cpp
diff --git a/Source/IO/NCFile.H b/Source/IO/REMORA_NCFile.H
similarity index 99%
rename from Source/IO/NCFile.H
rename to Source/IO/REMORA_NCFile.H
index 01f19277..7d69c41d 100644
--- a/Source/IO/NCFile.H
+++ b/Source/IO/REMORA_NCFile.H
@@ -1,5 +1,5 @@
-#ifndef _NCFILE_H_
-#define _NCFILE_H_
+#ifndef _REMORA_NCFILE_H_
+#define _REMORA_NCFILE_H_
 
 #include <sstream>
 #include <string>
@@ -9,7 +9,7 @@
 #include "AMReX_FArrayBox.H"
 #include "AMReX_IArrayBox.H"
 // this includes pnetcdf.h, and mpi.h
-#include "NCInterface.H"
+#include "REMORA_NCInterface.H"
 
 using PlaneVector = amrex::Vector<amrex::FArrayBox>;
 
diff --git a/Source/IO/NCFile.cpp b/Source/IO/REMORA_NCFile.cpp
similarity index 89%
rename from Source/IO/NCFile.cpp
rename to Source/IO/REMORA_NCFile.cpp
index 62d8eb3b..4e140352 100644
--- a/Source/IO/NCFile.cpp
+++ b/Source/IO/REMORA_NCFile.cpp
@@ -1,7 +1,7 @@
 #include <string>
 
-#include "NCFile.H"
-#include "NCInterface.H"
+#include "REMORA_NCFile.H"
+#include "REMORA_NCInterface.H"
 
 
 std::string ReadNetCDFVarAttrStr (const std::string& fname,
diff --git a/Source/IO/NCInterface.H b/Source/IO/REMORA_NCInterface.H
similarity index 99%
rename from Source/IO/NCInterface.H
rename to Source/IO/REMORA_NCInterface.H
index 2a2685e1..5f4854ae 100644
--- a/Source/IO/NCInterface.H
+++ b/Source/IO/REMORA_NCInterface.H
@@ -6,8 +6,8 @@
  *  OOP-like manner.
  */
 
-#ifndef NC_INTREMORAACE_H
-#define NC_INTREMORAACE_H
+#ifndef REMORA_NC_INTERFACE_H
+#define REMORA_NC_INTERFACE_H
 
 #ifdef REMORA_USE_NETCDF
 #include <string>
@@ -382,4 +382,4 @@ public:
 
 #endif
 
-#endif /* NC_INTREMORAACE_H */
+#endif /* NC_INTERFACE_H */
diff --git a/Source/IO/NCInterface.cpp b/Source/IO/REMORA_NCInterface.cpp
similarity index 99%
rename from Source/IO/NCInterface.cpp
rename to Source/IO/REMORA_NCInterface.cpp
index 77239241..8d5ca61c 100644
--- a/Source/IO/NCInterface.cpp
+++ b/Source/IO/REMORA_NCInterface.cpp
@@ -1,6 +1,6 @@
 #include <cstdio>
 
-#include "NCInterface.H"
+#include "REMORA_NCInterface.H"
 #include <AMReX.H>
 #include <AMReX_Print.H>
 
diff --git a/Source/IO/REMORA_NCPlotFile.H b/Source/IO/REMORA_NCPlotFile.H
new file mode 100644
index 00000000..31831ab9
--- /dev/null
+++ b/Source/IO/REMORA_NCPlotFile.H
@@ -0,0 +1,4 @@
+#ifndef _REMORA_NCPLOTFILE_H_
+#define _REMORA_NCPLOTFILE_H_
+extern std::string inputs_name;
+#endif
diff --git a/Source/IO/NCPlotFile.cpp b/Source/IO/REMORA_NCPlotFile.cpp
similarity index 99%
rename from Source/IO/NCPlotFile.cpp
rename to Source/IO/REMORA_NCPlotFile.cpp
index ff1cf154..2c33dea3 100644
--- a/Source/IO/NCPlotFile.cpp
+++ b/Source/IO/REMORA_NCPlotFile.cpp
@@ -12,9 +12,9 @@
 #include <AMReX_ParmParse.H>
 
 #include "REMORA.H"
-#include "NCInterface.H"
-#include "NCPlotFile.H"
-#include "IndexDefines.H"
+#include "REMORA_NCInterface.H"
+#include "REMORA_NCPlotFile.H"
+#include "REMORA_IndexDefines.H"
 
 using namespace amrex;
 
diff --git a/Source/IO/Plotfile.cpp b/Source/IO/REMORA_Plotfile.cpp
similarity index 99%
rename from Source/IO/Plotfile.cpp
rename to Source/IO/REMORA_Plotfile.cpp
index 1bd781dd..55ee6aa4 100644
--- a/Source/IO/Plotfile.cpp
+++ b/Source/IO/REMORA_Plotfile.cpp
@@ -1,4 +1,3 @@
-#include <EOS.H>
 #include <REMORA.H>
 #include "AMReX_Interp_3D_C.H"
 #include "AMReX_PlotFileUtil.H"
diff --git a/Source/IO/ReadFromBdryNetcdf.cpp b/Source/IO/REMORA_ReadFromBdryNetcdf.cpp
similarity index 99%
rename from Source/IO/ReadFromBdryNetcdf.cpp
rename to Source/IO/REMORA_ReadFromBdryNetcdf.cpp
index b31fd9eb..b5150734 100644
--- a/Source/IO/ReadFromBdryNetcdf.cpp
+++ b/Source/IO/REMORA_ReadFromBdryNetcdf.cpp
@@ -1,7 +1,7 @@
-#include "NCFile.H"
+#include "REMORA_NCFile.H"
 #include "AMReX_FArrayBox.H"
-#include "DataStruct.H"
-#include "IndexDefines.H"
+#include "REMORA_DataStruct.H"
+#include "REMORA_IndexDefines.H"
 
 using namespace amrex;
 
diff --git a/Source/IO/ReadFromInitNetcdf.cpp b/Source/IO/REMORA_ReadFromInitNetcdf.cpp
similarity index 99%
rename from Source/IO/ReadFromInitNetcdf.cpp
rename to Source/IO/REMORA_ReadFromInitNetcdf.cpp
index 4c377726..117bb9d4 100644
--- a/Source/IO/ReadFromInitNetcdf.cpp
+++ b/Source/IO/REMORA_ReadFromInitNetcdf.cpp
@@ -1,6 +1,6 @@
-#include "NCFile.H"
+#include "REMORA_NCFile.H"
 #include "AMReX_FArrayBox.H"
-#include "DataStruct.H"
+#include "REMORA_DataStruct.H"
 
 using namespace amrex;
 
diff --git a/Source/IO/console_io.cpp b/Source/IO/REMORA_console_io.cpp
similarity index 99%
rename from Source/IO/console_io.cpp
rename to Source/IO/REMORA_console_io.cpp
index dc5b3ab6..1c61960c 100644
--- a/Source/IO/console_io.cpp
+++ b/Source/IO/REMORA_console_io.cpp
@@ -5,7 +5,7 @@
 #include "AMReX_Vector.H"
 
 #ifdef REMORA_USE_NETCDF
-#include "NCInterface.H"
+#include "REMORA_NCInterface.H"
 #endif
 
 namespace amrex {
diff --git a/Source/IO/writeJobInfo.cpp b/Source/IO/REMORA_writeJobInfo.cpp
similarity index 100%
rename from Source/IO/writeJobInfo.cpp
rename to Source/IO/REMORA_writeJobInfo.cpp
diff --git a/Source/Initialization/Make.package b/Source/Initialization/Make.package
index 75db7462..7cf1c90c 100644
--- a/Source/Initialization/Make.package
+++ b/Source/Initialization/Make.package
@@ -1,5 +1,5 @@
 CEXE_sources += REMORA_init.cpp
-CEXE_headers += prob_common.H
+CEXE_headers += REMORA_prob_common.H
 
 CEXE_sources += REMORA_init_bcs.cpp
 CEXE_sources += REMORA_init1d.cpp
diff --git a/Source/Initialization/REMORA_init.cpp b/Source/Initialization/REMORA_init.cpp
index cd6cfc68..7aadf2da 100644
--- a/Source/Initialization/REMORA_init.cpp
+++ b/Source/Initialization/REMORA_init.cpp
@@ -3,9 +3,8 @@
  */
 
 #include <REMORA.H>
-#include <EOS.H>
 #include <REMORA_Constants.H>
-#include <prob_common.H>
+#include <REMORA_prob_common.H>
 
 using namespace amrex;
 
diff --git a/Source/Initialization/REMORA_init1d.cpp b/Source/Initialization/REMORA_init1d.cpp
index 31778b08..9e19eeaf 100644
--- a/Source/Initialization/REMORA_init1d.cpp
+++ b/Source/Initialization/REMORA_init1d.cpp
@@ -1,6 +1,5 @@
 #include <REMORA.H>
-#include <EOS.H>
-#include <prob_common.H>
+#include <REMORA_prob_common.H>
 
 using namespace amrex;
 
diff --git a/Source/Initialization/REMORA_init_from_netcdf.cpp b/Source/Initialization/REMORA_init_from_netcdf.cpp
index 49f5f126..73d5c756 100644
--- a/Source/Initialization/REMORA_init_from_netcdf.cpp
+++ b/Source/Initialization/REMORA_init_from_netcdf.cpp
@@ -3,10 +3,9 @@
  */
 
 #include <REMORA.H>
-#include <EOS.H>
 #include <REMORA_Constants.H>
-#include <prob_common.H>
-#include <DataStruct.H>
+#include <REMORA_prob_common.H>
+#include <REMORA_DataStruct.H>
 
 using namespace amrex;
 
diff --git a/Source/Initialization/REMORA_make_new_level.cpp b/Source/Initialization/REMORA_make_new_level.cpp
index fa451a72..6a744413 100644
--- a/Source/Initialization/REMORA_make_new_level.cpp
+++ b/Source/Initialization/REMORA_make_new_level.cpp
@@ -2,9 +2,8 @@
  * \file REMORA_make_new_level.cpp
  */
 
-#include <prob_common.H>
-#include <EOS.H>
 #include <REMORA.H>
+#include <REMORA_prob_common.H>
 
 #include <AMReX_buildInfo.H>
 
diff --git a/Source/Initialization/prob_common.H b/Source/Initialization/REMORA_prob_common.H
similarity index 95%
rename from Source/Initialization/prob_common.H
rename to Source/Initialization/REMORA_prob_common.H
index 844b2cff..0f5d03b3 100644
--- a/Source/Initialization/prob_common.H
+++ b/Source/Initialization/REMORA_prob_common.H
@@ -1,7 +1,7 @@
-#ifndef _PROBCOMMON_H_
-#define _PROBCOMMON_H_
+#ifndef _REMORA_PROBCOMMON_H_
+#define _REMORA_PROBCOMMON_H_
 
-#include <DataStruct.H>
+#include <REMORA_DataStruct.H>
 
 #include <AMReX_Geometry.H>
 #include <AMReX_FArrayBox.H>
diff --git a/Source/Make.package b/Source/Make.package
index bd73f177..25d2a05b 100644
--- a/Source/Make.package
+++ b/Source/Make.package
@@ -2,12 +2,12 @@ CEXE_sources += main.cpp
 CEXE_sources += REMORA.cpp
 CEXE_headers += REMORA.H
 
-CEXE_headers += IndexDefines.H
-CEXE_headers += EOS.H
-CEXE_headers += DataStruct.H
+CEXE_headers += REMORA_IndexDefines.H
+CEXE_headers += REMORA_EOS.H
+CEXE_headers += REMORA_DataStruct.H
 CEXE_headers += REMORA_Constants.H
 CEXE_sources += REMORA_Tagging.cpp
 CEXE_sources += REMORA_SumIQ.cpp
 
-CEXE_sources += Derive.cpp
-CEXE_headers += Derive.H
+CEXE_sources += REMORA_Derive.cpp
+CEXE_headers += REMORA_Derive.H
diff --git a/Source/Particles/Make.package b/Source/Particles/Make.package
index 89874885..9e70600c 100644
--- a/Source/Particles/Make.package
+++ b/Source/Particles/Make.package
@@ -3,5 +3,5 @@ CEXE_sources += REMORA_PC_Init.cpp
 CEXE_sources += REMORA_PC_Evolve.cpp
 CEXE_sources += REMORA_PC_Utils.cpp
 
-CEXE_headers += ParticleData.H
+CEXE_headers += REMORA_ParticleData.H
 CEXE_headers += REMORA_PC.H
diff --git a/Source/Particles/REMORA_PC_Evolve.cpp b/Source/Particles/REMORA_PC_Evolve.cpp
index 3f544a63..5fdb5f32 100644
--- a/Source/Particles/REMORA_PC_Evolve.cpp
+++ b/Source/Particles/REMORA_PC_Evolve.cpp
@@ -1,7 +1,7 @@
 #ifdef REMORA_USE_PARTICLES
 
 #include <REMORA_PC.H>
-#include <IndexDefines.H>
+#include <REMORA_IndexDefines.H>
 #include <REMORA_Constants.H>
 #include <AMReX_TracerParticle_mod_K.H>
 
diff --git a/Source/Particles/ParticleData.H b/Source/Particles/REMORA_ParticleData.H
similarity index 99%
rename from Source/Particles/ParticleData.H
rename to Source/Particles/REMORA_ParticleData.H
index 351383e2..b6fb0740 100644
--- a/Source/Particles/ParticleData.H
+++ b/Source/Particles/REMORA_ParticleData.H
@@ -1,5 +1,5 @@
-#ifndef _PARTICLE_DATA_H_
-#define _PARTICLE_DATA_H_
+#ifndef _REMORA_PARTICLE_DATA_H_
+#define _REMORA_PARTICLE_DATA_H_
 
 #ifdef REMORA_USE_PARTICLES
 
diff --git a/Source/REMORA.H b/Source/REMORA.H
index 265fc865..b9da02f4 100644
--- a/Source/REMORA.H
+++ b/Source/REMORA.H
@@ -30,17 +30,17 @@
 #include <REMORA_PhysBCFunct.H>
 #include <REMORA_FillPatcher.H>
 
-#include <IndexDefines.H>
-#include <TimeInterpolatedData.H>
-#include <DataStruct.H>
-#include <Derive.H>
+#include <REMORA_IndexDefines.H>
+#include <REMORA_TimeInterpolatedData.H>
+#include <REMORA_DataStruct.H>
+#include <REMORA_Derive.H>
 
 #ifdef REMORA_USE_PARTICLES
-#include "ParticleData.H"
+#include "REMORA_ParticleData.H"
 #endif
 
 #ifdef REMORA_USE_NETCDF
-#include "NCInterface.H"
+#include "REMORA_NCInterface.H"
 #endif
 
 #include <iostream>
diff --git a/Source/REMORA.cpp b/Source/REMORA.cpp
index c23cb24b..6df087ab 100644
--- a/Source/REMORA.cpp
+++ b/Source/REMORA.cpp
@@ -2,8 +2,7 @@
  * \file REMORA.cpp
  */
 
-#include <prob_common.H>
-#include <EOS.H>
+#include <REMORA_prob_common.H>
 #include <REMORA.H>
 
 #include <AMReX_buildInfo.H>
diff --git a/Source/DataStruct.H b/Source/REMORA_DataStruct.H
similarity index 99%
rename from Source/DataStruct.H
rename to Source/REMORA_DataStruct.H
index 8da7fef1..84daeb95 100644
--- a/Source/DataStruct.H
+++ b/Source/REMORA_DataStruct.H
@@ -1,5 +1,5 @@
-#ifndef _DATA_STRUCT_H_
-#define _DATA_STRUCT_H_
+#ifndef _REMORA_DATA_STRUCT_H_
+#define _REMORA_DATA_STRUCT_H_
 
 #include <string>
 #include <iostream>
@@ -9,7 +9,7 @@
 #include <AMReX_Gpu.H>
 
 #include <REMORA_Constants.H>
-#include "IndexDefines.H"
+#include "REMORA_IndexDefines.H"
 
 enum struct CouplingType {
     OneWay, TwoWay
diff --git a/Source/Derive.H b/Source/REMORA_Derive.H
similarity index 93%
rename from Source/Derive.H
rename to Source/REMORA_Derive.H
index 241d3bbe..cc337350 100644
--- a/Source/Derive.H
+++ b/Source/REMORA_Derive.H
@@ -1,5 +1,5 @@
-#ifndef _Derive_H_
-#define _Derive_H_
+#ifndef _REMORA_Derive_H_
+#define _REMORA_Derive_H_
 
 #include <AMReX_FArrayBox.H>
 #include <AMReX_Geometry.H>
diff --git a/Source/Derive.cpp b/Source/REMORA_Derive.cpp
similarity index 95%
rename from Source/Derive.cpp
rename to Source/REMORA_Derive.cpp
index 080030b4..36aacae3 100644
--- a/Source/Derive.cpp
+++ b/Source/REMORA_Derive.cpp
@@ -1,6 +1,5 @@
-#include "Derive.H"
-#include "EOS.H"
-#include "IndexDefines.H"
+#include "REMORA_Derive.H"
+#include "REMORA_IndexDefines.H"
 
 using namespace amrex;
 
diff --git a/Source/IndexDefines.H b/Source/REMORA_IndexDefines.H
similarity index 100%
rename from Source/IndexDefines.H
rename to Source/REMORA_IndexDefines.H
diff --git a/Source/REMORA_Tagging.cpp b/Source/REMORA_Tagging.cpp
index 24458f8d..cf35bfeb 100644
--- a/Source/REMORA_Tagging.cpp
+++ b/Source/REMORA_Tagging.cpp
@@ -1,5 +1,5 @@
 #include <REMORA.H>
-#include <Derive.H>
+#include <REMORA_Derive.H>
 
 using namespace amrex;
 
diff --git a/Source/TimeIntegration/REMORA_ComputeTimestep.cpp b/Source/TimeIntegration/REMORA_ComputeTimestep.cpp
index 1c2876e1..04414710 100644
--- a/Source/TimeIntegration/REMORA_ComputeTimestep.cpp
+++ b/Source/TimeIntegration/REMORA_ComputeTimestep.cpp
@@ -1,4 +1,3 @@
-#include <EOS.H>
 #include <REMORA.H>
 
 using namespace amrex;
diff --git a/Source/TimeIntegration/REMORA_set_weights.cpp b/Source/TimeIntegration/REMORA_set_weights.cpp
index 915cc1e8..e3071e1b 100644
--- a/Source/TimeIntegration/REMORA_set_weights.cpp
+++ b/Source/TimeIntegration/REMORA_set_weights.cpp
@@ -1,7 +1,7 @@
 #include <cmath>
-#include <DataStruct.H>
+#include <REMORA_DataStruct.H>
 #include <REMORA.H>
-#include <prob_common.H>
+#include <REMORA_prob_common.H>
 
 using namespace amrex;
 
diff --git a/Source/Utils/Make.package b/Source/Utils/Make.package
index 92bc3d3c..fcd24e69 100644
--- a/Source/Utils/Make.package
+++ b/Source/Utils/Make.package
@@ -1,2 +1,2 @@
 CEXE_headers += REMORA_Math.H
-CEXE_headers += DepthStretchTransform.H
+CEXE_headers += REMORA_DepthStretchTransform.H
diff --git a/Source/Utils/DepthStretchTransform.H b/Source/Utils/REMORA_DepthStretchTransform.H
similarity index 98%
rename from Source/Utils/DepthStretchTransform.H
rename to Source/Utils/REMORA_DepthStretchTransform.H
index 948e3c77..1f7accd8 100644
--- a/Source/Utils/DepthStretchTransform.H
+++ b/Source/Utils/REMORA_DepthStretchTransform.H
@@ -1,10 +1,10 @@
-#ifndef STRETCH_H_
-#define STRETCH_H_
+#ifndef _REMORA_STRETCH_H_
+#define _REMORA_STRETCH_H_
 
 #include <cmath>
-#include <DataStruct.H>
+#include <REMORA_DataStruct.H>
 #include <REMORA.H>
-#include <prob_common.H>
+#include <REMORA_prob_common.H>
 
 using namespace amrex;