[MOAB-dev] commit/MOAB: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Jun 5 13:09:37 CDT 2013
3 new commits in MOAB:
https://bitbucket.org/fathomteam/moab/commits/830bae48d199/
Changeset: 830bae48d199
Branch: None
User: danwu
Date: 2013-06-05 18:53:12
Summary: Merged fathomteam/moab into master
Affected #: 1 file
diff --git a/config/compiler.m4 b/config/compiler.m4
index 81596a6..6a7e2ed 100644
--- a/config/compiler.m4
+++ b/config/compiler.m4
@@ -102,15 +102,27 @@ if test "xno" != "x$WITH_MPI"; then
DISTCHECK_CONFIGURE_FLAGS="$DISTCHECK_CONFIGURE_FLAGS --with-mpi=\"${withval}\""
if test "xyes" == "x$WITH_MPI"; then
+ if test "xno" != "x$CHECK_CC"; then
FATHOM_SET_MPI_COMPILER([CC], [$CC_LIST])
+ fi
+ if test "xno" != "x$CHECK_CXX"; then
FATHOM_SET_MPI_COMPILER([CXX],[$CXX_LIST])
- FATHOM_SET_MPI_COMPILER([FC], [$FC_LIST])
- FATHOM_SET_MPI_COMPILER([F77],[$F77_LIST])
+ fi
+ if test "xno" != "x$CHECK_FC"; then
+ FATHOM_SET_MPI_COMPILER([FC], [$FC_LIST])
+ FATHOM_SET_MPI_COMPILER([F77],[$F77_LIST])
+ fi
else
+ if test "xno" != "x$CHECK_CC"; then
FATHOM_SET_MPI_COMPILER([CC], [$CC_LIST],[${WITH_MPI}/bin])
+ fi
+ if test "xno" != "x$CHECK_CXX"; then
FATHOM_SET_MPI_COMPILER([CXX],[$CXX_LIST],[${WITH_MPI}/bin])
- FATHOM_SET_MPI_COMPILER([FC], [$FC_LIST],[${WITH_MPI}/bin])
- FATHOM_SET_MPI_COMPILER([F77],[$F77_LIST],[${WITH_MPI}/bin])
+ fi
+ if test "xno" != "x$CHECK_FC"; then
+ FATHOM_SET_MPI_COMPILER([FC], [$FC_LIST],[${WITH_MPI}/bin])
+ FATHOM_SET_MPI_COMPILER([F77],[$F77_LIST],[${WITH_MPI}/bin])
+ fi
WITH_MPI=yes
fi
fi
https://bitbucket.org/fathomteam/moab/commits/616f193a6bae/
Changeset: 616f193a6bae
Branch: None
User: danwu
Date: 2013-06-05 19:51:28
Summary: Small changes after refactoring of ReadNC class
Affected #: 4 files
diff --git a/src/io/NCHelperEuler.cpp b/src/io/NCHelperEuler.cpp
index 9346d22..a01d4b8 100644
--- a/src/io/NCHelperEuler.cpp
+++ b/src/io/NCHelperEuler.cpp
@@ -19,7 +19,7 @@ bool NCHelperEuler::can_read_file(ReadNC* readNC, int fileId)
// If dimension names "lon" AND "lat' exist then it could be either the Eulerian Spectral grid or the FV grid
if ((std::find(dimNames.begin(), dimNames.end(), std::string("lon")) != dimNames.end()) && (std::find(dimNames.begin(),
- dimNames.end(), std::string("lat")) != dimNames.end())) {
+ dimNames.end(), std::string("lat")) != dimNames.end())) {
// If dimension names "lon" AND "lat" AND "slon" AND "slat" exist then it should be the FV grid
if ((std::find(dimNames.begin(), dimNames.end(), std::string("slon")) != dimNames.end()) && (std::find(dimNames.begin(),
dimNames.end(), std::string("slat")) != dimNames.end()))
diff --git a/src/io/NCHelperFV.cpp b/src/io/NCHelperFV.cpp
index b086102..566b719 100644
--- a/src/io/NCHelperFV.cpp
+++ b/src/io/NCHelperFV.cpp
@@ -19,7 +19,7 @@ bool NCHelperFV::can_read_file(ReadNC* readNC, int fileId)
dimNames.end(), std::string("lat")) != dimNames.end()) && (std::find(dimNames.begin(), dimNames.end(), std::string("slon"))
!= dimNames.end()) && (std::find(dimNames.begin(), dimNames.end(), std::string("slat")) != dimNames.end())) {
// Make sure it is CAM grid
- std::map<std::string, ReadNC::AttData>::iterator attIt = readNC->globalAtts.find("source");
+ std::map<std::string, ReadNC::AttData>::iterator attIt = readNC->globalAtts.find("source");
if (attIt == readNC->globalAtts.end()) {
readNC->readMeshIface->report_error("%s", "File does not have source global attribute.");
return false;
diff --git a/src/io/ReadNC.cpp b/src/io/ReadNC.cpp
index 8c77431..514f724 100644
--- a/src/io/ReadNC.cpp
+++ b/src/io/ReadNC.cpp
@@ -41,7 +41,7 @@ ReadNC::ReadNC(Interface* impl) :
#ifdef USE_MPI
myPcomm(NULL),
#endif
- noMesh(false), noVars(false), spectralMesh(false), helper(NULL)
+ noMesh(false), noVars(false), spectralMesh(false), myHelper(NULL)
{
assert(impl != NULL);
@@ -90,8 +90,8 @@ void ReadNC::reset() {
ReadNC::~ReadNC() {
mbImpl->release_interface(readMeshIface);
- if (helper != NULL)
- delete helper;
+ if (myHelper != NULL)
+ delete myHelper;
}
ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set, const FileOptions& opts,
@@ -194,15 +194,15 @@ ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set,
ERRORR(MB_FAILURE, "File not following known conventions.");
}
- if (helper != NULL)
- delete helper;
+ if (myHelper != NULL)
+ delete myHelper;
- helper = NCHelper::get_nc_helper(this, fileId, opts);
- if (helper == NULL) {
+ myHelper = NCHelper::get_nc_helper(this, fileId, opts);
+ if (myHelper == NULL) {
ERRORR(MB_FAILURE, "Failed to get NCHelper class instance.");
}
- rval = helper->init_mesh_vals(opts, tmp_set);
+ rval = myHelper->init_mesh_vals(opts, tmp_set);
ERRORR(rval, "Trouble initializing mesh values.");
// Create mesh vertex/quads sequences
@@ -212,15 +212,15 @@ ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set,
ERRORR(rval, "Mesh characteristics didn't match from last read.\n");
}
else if (!noMesh) {
- rval = helper->create_verts_quads(scdi, opts, tmp_set, quads);
+ rval = myHelper->create_verts_quads(scdi, opts, tmp_set, quads);
ERRORR(rval, "Trouble creating vertices and quads.");
}
- bool scdMesh = helper->is_scd_mesh();
+ bool scd_mesh = myHelper->is_scd_mesh();
// Read variables onto grid
if (!noVars) {
- rval = read_variables(tmp_set, var_names, tstep_nums, scdMesh);
+ rval = read_variables(tmp_set, var_names, tstep_nums, scd_mesh);
if (MB_FAILURE == rval)
return rval;
}
@@ -232,7 +232,7 @@ ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set,
if (mit != varInfo.end())
filteredDimNames.push_back(dimNames[i]);
}
- rval = read_variables(tmp_set, filteredDimNames, tstep_nums, scdMesh);
+ rval = read_variables(tmp_set, filteredDimNames, tstep_nums, scd_mesh);
if (MB_FAILURE == rval)
return rval;
}
@@ -593,10 +593,10 @@ ErrorCode ReadNC::create_scd_verts_quads(ScdInterface *scdi, EntityHandle tmp_se
}
ErrorCode ReadNC::read_variable_setup(std::vector<std::string> &var_names, std::vector<int> &tstep_nums,
- std::vector<VarData> &vdatas, std::vector<VarData> &vsetdatas, bool scdMesh) {
+ std::vector<VarData> &vdatas, std::vector<VarData> &vsetdatas, bool scd_mesh) {
std::map<std::string, VarData>::iterator mit;
- if (scdMesh) { // scd mesh
+ if (scd_mesh) { // scd mesh
// if empty read them all
if (var_names.empty()) {
for (mit = varInfo.begin(); mit != varInfo.end(); mit++) {
@@ -697,7 +697,7 @@ ErrorCode ReadNC::read_variable_setup(std::vector<std::string> &var_names, std::
return MB_SUCCESS;
}
-ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scdMesh) {
+ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scd_mesh) {
ErrorCode rval = MB_SUCCESS;
std::vector<EntityHandle>* ehandles = NULL;
@@ -795,7 +795,7 @@ ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarD
switch (vdatas[i].entLoc) {
case 0:
// vertices
- if (scdMesh) {
+ if (scd_mesh) {
// only structured mesh has j parameter that multiplies i to get total # vertices
vdatas[i].readDims[t].push_back(lDims[1]);
vdatas[i].readCounts[t].push_back(lDims[4] - lDims[1] + 1);
@@ -897,33 +897,33 @@ ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarD
return rval;
}
-ErrorCode ReadNC::read_variables(EntityHandle file_set, std::vector<std::string> &var_names, std::vector<int> &tstep_nums, bool scdMesh) {
+ErrorCode ReadNC::read_variables(EntityHandle file_set, std::vector<std::string> &var_names, std::vector<int> &tstep_nums, bool scd_mesh) {
std::vector<VarData> vdatas;
std::vector<VarData> vsetdatas;
- ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas, scdMesh);
+ ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas, scd_mesh);
ERRORR(rval, "Trouble setting up read variable.");
- if (scdMesh) {
+ if (scd_mesh) {
// create COORDS tag for quads
rval = create_quad_coordinate_tag(file_set);
ERRORR(rval, "Trouble creating coordinate tags to entities quads");
}
if (!vsetdatas.empty()) {
- rval = read_variable_to_set(file_set, vsetdatas, tstep_nums, scdMesh);
+ rval = read_variable_to_set(file_set, vsetdatas, tstep_nums, scd_mesh);
ERRORR(rval, "Trouble read variables to set.");
}
if (!vdatas.empty()) {
#ifdef PNETCDF_FILE
- if (!scdMesh) // in serial, we will use the old read, everything is contiguous
+ if (!scd_mesh) // in serial, we will use the old read, everything is contiguous
// in parallel, we will use async read in pnetcdf
// the other mechanism is not working, forget about it
rval = read_variable_to_nonset_async(file_set, vdatas, tstep_nums);
else
#endif
- rval = read_variable_to_nonset(file_set, vdatas, tstep_nums, scdMesh);
+ rval = read_variable_to_nonset(file_set, vdatas, tstep_nums, scd_mesh);
ERRORR(rval, "Trouble read variables to entities verts/edges/quads.");
}
@@ -1011,7 +1011,7 @@ ErrorCode ReadNC::read_variable_to_set_allocate(std::vector<VarData> &vdatas, st
return rval;
}
-ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scdMesh) {
+ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scd_mesh) {
ErrorCode rval = read_variable_to_set_allocate(vdatas, tstep_nums);
ERRORR(rval, "Trouble allocating read variables to set.");
@@ -1075,7 +1075,7 @@ ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarDat
for (unsigned int i = 0; i < vdatas.size(); i++) {
for (unsigned int t = 0; t < tstep_nums.size(); t++) {
dbgOut.tprintf(2, "Converting variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]);
- ErrorCode tmp_rval = convert_variable(vdatas[i], t, scdMesh);
+ ErrorCode tmp_rval = convert_variable(vdatas[i], t, scd_mesh);
if (MB_SUCCESS != tmp_rval)
rval = tmp_rval;
if (vdatas[i].varDims.size() <= 1)
@@ -1104,8 +1104,8 @@ ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarDat
return rval;
}
-ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scdMesh) {
- ErrorCode rval = read_variable_allocate(file_set, vdatas, tstep_nums, scdMesh);
+ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scd_mesh) {
+ ErrorCode rval = read_variable_allocate(file_set, vdatas, tstep_nums, scd_mesh);
ERRORR(rval, "Trouble allocating read variables.");
// finally, read into that space
@@ -1116,7 +1116,7 @@ ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<Var
void *data = vdatas[i].varDatas[t];
std::size_t sz = 1;
size_t ni = vdatas[i].readCounts[t][2], nj = vdatas[i].readCounts[t][3], nk = vdatas[i].readCounts[t][1];
- if (scdMesh) {
+ if (scd_mesh) {
for (std::size_t idx = 0; idx != vdatas[i].readCounts[t].size(); ++idx)
sz *= vdatas[i].readCounts[t][idx];
}
@@ -1158,7 +1158,7 @@ ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<Var
case NC_FLOAT: {
std::vector<float> tmpfloatdata(sz);
- if (scdMesh)
+ if (scd_mesh)
{
success = NCFUNCAG(_vara_float)(fileId, vdatas[i].varId, &vdatas[i].readDims[t][0], &vdatas[i].readCounts[t][0],
&tmpfloatdata[0] NCREQ);
@@ -1252,7 +1252,7 @@ ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<Var
for (unsigned int i = 0; i < vdatas.size(); i++) {
for (unsigned int t = 0; t < tstep_nums.size(); t++) {
dbgOut.tprintf(2, "Converting variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]);
- ErrorCode tmp_rval = convert_variable(vdatas[i], t, scdMesh);
+ ErrorCode tmp_rval = convert_variable(vdatas[i], t, scd_mesh);
if (MB_SUCCESS != tmp_rval)
rval = tmp_rval;
}
@@ -1440,12 +1440,12 @@ ErrorCode ReadNC::read_variable_to_nonset_async(EntityHandle file_set, std::vect
}
#endif
-ErrorCode ReadNC::convert_variable(VarData &var_data, int tstep_num, bool scdMesh) {
+ErrorCode ReadNC::convert_variable(VarData &var_data, int tstep_num, bool scd_mesh) {
// get ptr to tag space
void *data = var_data.varDatas[tstep_num];
std::size_t sz = 1;
- if (scdMesh) {
+ if (scd_mesh) {
for (std::size_t idx = 0; idx != var_data.readCounts[tstep_num].size(); ++idx)
sz *= var_data.readCounts[tstep_num][idx];
}
@@ -2022,7 +2022,7 @@ ErrorCode ReadNC::create_tags(ScdInterface *scdi, EntityHandle file_set, const s
// <__MESH_TYPE>
Tag meshTypeTag = 0;
tag_name = "__MESH_TYPE";
- std::string meshTypeName = helper->get_mesh_type_name();
+ std::string meshTypeName = myHelper->get_mesh_type_name();
rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN);
ERRORR(rval, "Trouble creating __MESH_TYPE tag.");
diff --git a/src/io/ReadNC.hpp b/src/io/ReadNC.hpp
index 87ed049..cd1ca6b 100644
--- a/src/io/ReadNC.hpp
+++ b/src/io/ReadNC.hpp
@@ -176,10 +176,10 @@ private:
std::vector<int> &tstep_nums);
ErrorCode read_variable_to_set(EntityHandle file_set, std::vector<VarData> &vdatas,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
ErrorCode read_variable_to_nonset(EntityHandle file_set, std::vector<VarData> &vdatas,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
#ifdef PNETCDF_FILE
ErrorCode read_variable_to_nonset_async(EntityHandle file_set, std::vector<VarData> &vdatas,
@@ -187,18 +187,18 @@ private:
#endif
ErrorCode read_variables(EntityHandle file_set, std::vector<std::string> &var_names,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
ErrorCode read_variable_allocate(EntityHandle file_set, std::vector<VarData> &vdatas,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
ErrorCode read_variable_setup(std::vector<std::string> &var_names,
std::vector<int> &tstep_nums,
std::vector<VarData> &vdatas,
std::vector<VarData> &vsetdatas,
- bool scdMesh);
+ bool scd_mesh);
- ErrorCode convert_variable(VarData &var_data, int tstep_num, bool scdMesh);
+ ErrorCode convert_variable(VarData &var_data, int tstep_num, bool scd_mesh);
ErrorCode get_tag_to_set(VarData &var_data, int tstep_num, Tag &tagh);
@@ -387,7 +387,7 @@ private:
std::string partitionTagName;
//! Helper class instance
- NCHelper* helper;
+ NCHelper* myHelper;
};
// inline functions
https://bitbucket.org/fathomteam/moab/commits/44c9debf15e5/
Changeset: 44c9debf15e5
Branch: master
User: tautges
Date: 2013-06-05 20:09:30
Summary: Merged in danwu/moab (pull request #6)
Minor code changes for ReadNC and NCHelper
Affected #: 4 files
diff --git a/src/io/NCHelperEuler.cpp b/src/io/NCHelperEuler.cpp
index 9346d22..a01d4b8 100644
--- a/src/io/NCHelperEuler.cpp
+++ b/src/io/NCHelperEuler.cpp
@@ -19,7 +19,7 @@ bool NCHelperEuler::can_read_file(ReadNC* readNC, int fileId)
// If dimension names "lon" AND "lat' exist then it could be either the Eulerian Spectral grid or the FV grid
if ((std::find(dimNames.begin(), dimNames.end(), std::string("lon")) != dimNames.end()) && (std::find(dimNames.begin(),
- dimNames.end(), std::string("lat")) != dimNames.end())) {
+ dimNames.end(), std::string("lat")) != dimNames.end())) {
// If dimension names "lon" AND "lat" AND "slon" AND "slat" exist then it should be the FV grid
if ((std::find(dimNames.begin(), dimNames.end(), std::string("slon")) != dimNames.end()) && (std::find(dimNames.begin(),
dimNames.end(), std::string("slat")) != dimNames.end()))
diff --git a/src/io/NCHelperFV.cpp b/src/io/NCHelperFV.cpp
index b086102..566b719 100644
--- a/src/io/NCHelperFV.cpp
+++ b/src/io/NCHelperFV.cpp
@@ -19,7 +19,7 @@ bool NCHelperFV::can_read_file(ReadNC* readNC, int fileId)
dimNames.end(), std::string("lat")) != dimNames.end()) && (std::find(dimNames.begin(), dimNames.end(), std::string("slon"))
!= dimNames.end()) && (std::find(dimNames.begin(), dimNames.end(), std::string("slat")) != dimNames.end())) {
// Make sure it is CAM grid
- std::map<std::string, ReadNC::AttData>::iterator attIt = readNC->globalAtts.find("source");
+ std::map<std::string, ReadNC::AttData>::iterator attIt = readNC->globalAtts.find("source");
if (attIt == readNC->globalAtts.end()) {
readNC->readMeshIface->report_error("%s", "File does not have source global attribute.");
return false;
diff --git a/src/io/ReadNC.cpp b/src/io/ReadNC.cpp
index 8c77431..514f724 100644
--- a/src/io/ReadNC.cpp
+++ b/src/io/ReadNC.cpp
@@ -41,7 +41,7 @@ ReadNC::ReadNC(Interface* impl) :
#ifdef USE_MPI
myPcomm(NULL),
#endif
- noMesh(false), noVars(false), spectralMesh(false), helper(NULL)
+ noMesh(false), noVars(false), spectralMesh(false), myHelper(NULL)
{
assert(impl != NULL);
@@ -90,8 +90,8 @@ void ReadNC::reset() {
ReadNC::~ReadNC() {
mbImpl->release_interface(readMeshIface);
- if (helper != NULL)
- delete helper;
+ if (myHelper != NULL)
+ delete myHelper;
}
ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set, const FileOptions& opts,
@@ -194,15 +194,15 @@ ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set,
ERRORR(MB_FAILURE, "File not following known conventions.");
}
- if (helper != NULL)
- delete helper;
+ if (myHelper != NULL)
+ delete myHelper;
- helper = NCHelper::get_nc_helper(this, fileId, opts);
- if (helper == NULL) {
+ myHelper = NCHelper::get_nc_helper(this, fileId, opts);
+ if (myHelper == NULL) {
ERRORR(MB_FAILURE, "Failed to get NCHelper class instance.");
}
- rval = helper->init_mesh_vals(opts, tmp_set);
+ rval = myHelper->init_mesh_vals(opts, tmp_set);
ERRORR(rval, "Trouble initializing mesh values.");
// Create mesh vertex/quads sequences
@@ -212,15 +212,15 @@ ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set,
ERRORR(rval, "Mesh characteristics didn't match from last read.\n");
}
else if (!noMesh) {
- rval = helper->create_verts_quads(scdi, opts, tmp_set, quads);
+ rval = myHelper->create_verts_quads(scdi, opts, tmp_set, quads);
ERRORR(rval, "Trouble creating vertices and quads.");
}
- bool scdMesh = helper->is_scd_mesh();
+ bool scd_mesh = myHelper->is_scd_mesh();
// Read variables onto grid
if (!noVars) {
- rval = read_variables(tmp_set, var_names, tstep_nums, scdMesh);
+ rval = read_variables(tmp_set, var_names, tstep_nums, scd_mesh);
if (MB_FAILURE == rval)
return rval;
}
@@ -232,7 +232,7 @@ ErrorCode ReadNC::load_file(const char *file_name, const EntityHandle* file_set,
if (mit != varInfo.end())
filteredDimNames.push_back(dimNames[i]);
}
- rval = read_variables(tmp_set, filteredDimNames, tstep_nums, scdMesh);
+ rval = read_variables(tmp_set, filteredDimNames, tstep_nums, scd_mesh);
if (MB_FAILURE == rval)
return rval;
}
@@ -593,10 +593,10 @@ ErrorCode ReadNC::create_scd_verts_quads(ScdInterface *scdi, EntityHandle tmp_se
}
ErrorCode ReadNC::read_variable_setup(std::vector<std::string> &var_names, std::vector<int> &tstep_nums,
- std::vector<VarData> &vdatas, std::vector<VarData> &vsetdatas, bool scdMesh) {
+ std::vector<VarData> &vdatas, std::vector<VarData> &vsetdatas, bool scd_mesh) {
std::map<std::string, VarData>::iterator mit;
- if (scdMesh) { // scd mesh
+ if (scd_mesh) { // scd mesh
// if empty read them all
if (var_names.empty()) {
for (mit = varInfo.begin(); mit != varInfo.end(); mit++) {
@@ -697,7 +697,7 @@ ErrorCode ReadNC::read_variable_setup(std::vector<std::string> &var_names, std::
return MB_SUCCESS;
}
-ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scdMesh) {
+ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scd_mesh) {
ErrorCode rval = MB_SUCCESS;
std::vector<EntityHandle>* ehandles = NULL;
@@ -795,7 +795,7 @@ ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarD
switch (vdatas[i].entLoc) {
case 0:
// vertices
- if (scdMesh) {
+ if (scd_mesh) {
// only structured mesh has j parameter that multiplies i to get total # vertices
vdatas[i].readDims[t].push_back(lDims[1]);
vdatas[i].readCounts[t].push_back(lDims[4] - lDims[1] + 1);
@@ -897,33 +897,33 @@ ErrorCode ReadNC::read_variable_allocate(EntityHandle file_set, std::vector<VarD
return rval;
}
-ErrorCode ReadNC::read_variables(EntityHandle file_set, std::vector<std::string> &var_names, std::vector<int> &tstep_nums, bool scdMesh) {
+ErrorCode ReadNC::read_variables(EntityHandle file_set, std::vector<std::string> &var_names, std::vector<int> &tstep_nums, bool scd_mesh) {
std::vector<VarData> vdatas;
std::vector<VarData> vsetdatas;
- ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas, scdMesh);
+ ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas, scd_mesh);
ERRORR(rval, "Trouble setting up read variable.");
- if (scdMesh) {
+ if (scd_mesh) {
// create COORDS tag for quads
rval = create_quad_coordinate_tag(file_set);
ERRORR(rval, "Trouble creating coordinate tags to entities quads");
}
if (!vsetdatas.empty()) {
- rval = read_variable_to_set(file_set, vsetdatas, tstep_nums, scdMesh);
+ rval = read_variable_to_set(file_set, vsetdatas, tstep_nums, scd_mesh);
ERRORR(rval, "Trouble read variables to set.");
}
if (!vdatas.empty()) {
#ifdef PNETCDF_FILE
- if (!scdMesh) // in serial, we will use the old read, everything is contiguous
+ if (!scd_mesh) // in serial, we will use the old read, everything is contiguous
// in parallel, we will use async read in pnetcdf
// the other mechanism is not working, forget about it
rval = read_variable_to_nonset_async(file_set, vdatas, tstep_nums);
else
#endif
- rval = read_variable_to_nonset(file_set, vdatas, tstep_nums, scdMesh);
+ rval = read_variable_to_nonset(file_set, vdatas, tstep_nums, scd_mesh);
ERRORR(rval, "Trouble read variables to entities verts/edges/quads.");
}
@@ -1011,7 +1011,7 @@ ErrorCode ReadNC::read_variable_to_set_allocate(std::vector<VarData> &vdatas, st
return rval;
}
-ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scdMesh) {
+ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scd_mesh) {
ErrorCode rval = read_variable_to_set_allocate(vdatas, tstep_nums);
ERRORR(rval, "Trouble allocating read variables to set.");
@@ -1075,7 +1075,7 @@ ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarDat
for (unsigned int i = 0; i < vdatas.size(); i++) {
for (unsigned int t = 0; t < tstep_nums.size(); t++) {
dbgOut.tprintf(2, "Converting variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]);
- ErrorCode tmp_rval = convert_variable(vdatas[i], t, scdMesh);
+ ErrorCode tmp_rval = convert_variable(vdatas[i], t, scd_mesh);
if (MB_SUCCESS != tmp_rval)
rval = tmp_rval;
if (vdatas[i].varDims.size() <= 1)
@@ -1104,8 +1104,8 @@ ErrorCode ReadNC::read_variable_to_set(EntityHandle file_set, std::vector<VarDat
return rval;
}
-ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scdMesh) {
- ErrorCode rval = read_variable_allocate(file_set, vdatas, tstep_nums, scdMesh);
+ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<VarData> &vdatas, std::vector<int> &tstep_nums, bool scd_mesh) {
+ ErrorCode rval = read_variable_allocate(file_set, vdatas, tstep_nums, scd_mesh);
ERRORR(rval, "Trouble allocating read variables.");
// finally, read into that space
@@ -1116,7 +1116,7 @@ ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<Var
void *data = vdatas[i].varDatas[t];
std::size_t sz = 1;
size_t ni = vdatas[i].readCounts[t][2], nj = vdatas[i].readCounts[t][3], nk = vdatas[i].readCounts[t][1];
- if (scdMesh) {
+ if (scd_mesh) {
for (std::size_t idx = 0; idx != vdatas[i].readCounts[t].size(); ++idx)
sz *= vdatas[i].readCounts[t][idx];
}
@@ -1158,7 +1158,7 @@ ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<Var
case NC_FLOAT: {
std::vector<float> tmpfloatdata(sz);
- if (scdMesh)
+ if (scd_mesh)
{
success = NCFUNCAG(_vara_float)(fileId, vdatas[i].varId, &vdatas[i].readDims[t][0], &vdatas[i].readCounts[t][0],
&tmpfloatdata[0] NCREQ);
@@ -1252,7 +1252,7 @@ ErrorCode ReadNC::read_variable_to_nonset(EntityHandle file_set, std::vector<Var
for (unsigned int i = 0; i < vdatas.size(); i++) {
for (unsigned int t = 0; t < tstep_nums.size(); t++) {
dbgOut.tprintf(2, "Converting variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]);
- ErrorCode tmp_rval = convert_variable(vdatas[i], t, scdMesh);
+ ErrorCode tmp_rval = convert_variable(vdatas[i], t, scd_mesh);
if (MB_SUCCESS != tmp_rval)
rval = tmp_rval;
}
@@ -1440,12 +1440,12 @@ ErrorCode ReadNC::read_variable_to_nonset_async(EntityHandle file_set, std::vect
}
#endif
-ErrorCode ReadNC::convert_variable(VarData &var_data, int tstep_num, bool scdMesh) {
+ErrorCode ReadNC::convert_variable(VarData &var_data, int tstep_num, bool scd_mesh) {
// get ptr to tag space
void *data = var_data.varDatas[tstep_num];
std::size_t sz = 1;
- if (scdMesh) {
+ if (scd_mesh) {
for (std::size_t idx = 0; idx != var_data.readCounts[tstep_num].size(); ++idx)
sz *= var_data.readCounts[tstep_num][idx];
}
@@ -2022,7 +2022,7 @@ ErrorCode ReadNC::create_tags(ScdInterface *scdi, EntityHandle file_set, const s
// <__MESH_TYPE>
Tag meshTypeTag = 0;
tag_name = "__MESH_TYPE";
- std::string meshTypeName = helper->get_mesh_type_name();
+ std::string meshTypeName = myHelper->get_mesh_type_name();
rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN);
ERRORR(rval, "Trouble creating __MESH_TYPE tag.");
diff --git a/src/io/ReadNC.hpp b/src/io/ReadNC.hpp
index 87ed049..cd1ca6b 100644
--- a/src/io/ReadNC.hpp
+++ b/src/io/ReadNC.hpp
@@ -176,10 +176,10 @@ private:
std::vector<int> &tstep_nums);
ErrorCode read_variable_to_set(EntityHandle file_set, std::vector<VarData> &vdatas,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
ErrorCode read_variable_to_nonset(EntityHandle file_set, std::vector<VarData> &vdatas,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
#ifdef PNETCDF_FILE
ErrorCode read_variable_to_nonset_async(EntityHandle file_set, std::vector<VarData> &vdatas,
@@ -187,18 +187,18 @@ private:
#endif
ErrorCode read_variables(EntityHandle file_set, std::vector<std::string> &var_names,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
ErrorCode read_variable_allocate(EntityHandle file_set, std::vector<VarData> &vdatas,
- std::vector<int> &tstep_nums, bool scdMesh);
+ std::vector<int> &tstep_nums, bool scd_mesh);
ErrorCode read_variable_setup(std::vector<std::string> &var_names,
std::vector<int> &tstep_nums,
std::vector<VarData> &vdatas,
std::vector<VarData> &vsetdatas,
- bool scdMesh);
+ bool scd_mesh);
- ErrorCode convert_variable(VarData &var_data, int tstep_num, bool scdMesh);
+ ErrorCode convert_variable(VarData &var_data, int tstep_num, bool scd_mesh);
ErrorCode get_tag_to_set(VarData &var_data, int tstep_num, Tag &tagh);
@@ -387,7 +387,7 @@ private:
std::string partitionTagName;
//! Helper class instance
- NCHelper* helper;
+ NCHelper* myHelper;
};
// inline functions
Repository URL: https://bitbucket.org/fathomteam/moab/
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