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qiangshuqiangshu
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change to add interfacial nodes as interdomain ghost nodes. Thus only minimal change original schism uncombined file
is needed. Add 3d prism bottom index to plot prism center data correctly.
1 parent 7a0051a commit baa3542

7 files changed

Lines changed: 365 additions & 48 deletions

‎mdschism/MDSCHISMOutput.cpp‎

Lines changed: 95 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@ MDSchismOutput::MDSchismOutput(const std::string a_outputFile,const std::string
1919
m_face_bottom(NULL),
2020
m_node_bottom(NULL),
2121
m_edge_bottom(NULL),
22+
m_prism_bottom(NULL),
2223
m_face_nodes(NULL),
2324
m_side_nodes(NULL),
2425
m_face_bottom_time_id(-1),
@@ -105,6 +106,10 @@ MDSchismOutput::~MDSchismOutput()
105106
delete m_edge_bottom;
106107
}
107108

109+
if (m_prism_bottom)
110+
{
111+
delete m_edge_bottom;
112+
}
108113
if(m_side_nodes)
109114
{
110115
delete m_side_nodes;
@@ -341,6 +346,19 @@ void MDSchismOutput::get_face_bottom(int* a_face_bottom,const int& a_time)
341346
a_face_bottom[i]=m_face_bottom[i];
342347
}
343348
}
349+
350+
void MDSchismOutput::get_prism_bottom(int* a_prism_bottom, const int& a_time)
351+
{
352+
NcDim * dimFacePtr = m_outputNcFilePtr->get_dim(MeshConstants10::DIM_MESH_FACES.c_str());
353+
long numMeshFaces = 0;
354+
numMeshFaces = dimFacePtr->size();
355+
356+
for (long i = 0; i < numMeshFaces; i++)
357+
{
358+
a_prism_bottom[i] = m_prism_bottom[i];
359+
}
360+
}
361+
344362
void MDSchismOutput::get_edge_bottom(int* a_edge_bottom,const int& a_time)
345363
{
346364
NcDim * dimEdgePtr = m_outputNcFilePtr->get_dim(MeshConstants10::DIM_MESH_EDGES.c_str());
@@ -491,6 +509,38 @@ void MDSchismOutput::update_ele_bottom(const int& a_time,int* a_node_bottom)
491509

492510
}
493511

512+
void MDSchismOutput::set_prism_bottom(const int& a_time, int* a_prism_bottom)
513+
{
514+
update_prism_bottom(a_time, a_prism_bottom);
515+
}
516+
517+
void MDSchismOutput::update_prism_bottom(const int& a_time, int* a_prism_bottom)
518+
{
519+
520+
NcDim * dimFacePtr = m_outputNcFilePtr->get_dim(MeshConstants10::DIM_MESH_FACES.c_str());
521+
long numMeshFaces = 0;
522+
numMeshFaces = dimFacePtr->size();
523+
NcDim * dimNodePtr = m_outputNcFilePtr->get_dim(MeshConstants10::DIM_MESH_NODES.c_str());
524+
long numMeshNodes = 0;
525+
numMeshNodes = dimNodePtr->size();
526+
527+
528+
if (!(m_prism_bottom))
529+
{
530+
m_prism_bottom = new int[numMeshFaces];
531+
}
532+
533+
for (long iface = 0; iface < numMeshFaces; iface++)
534+
{
535+
536+
m_prism_bottom[iface] = a_prism_bottom[iface];
537+
538+
}
539+
m_prism_bottom_time_id = a_time;
540+
541+
}
542+
543+
494544

495545
bool MDSchismOutput::load_dim_var()
496546
{
@@ -580,13 +630,43 @@ bool MDSchismOutput::load_dim_var()
580630

581631
std::string nc_att_name(att_var->name());
582632

583-
if ((!(nc_att_name.compare(MeshConstants10::CENTER)))||(!(nc_att_name.compare(MeshConstants10::LOCATION))))
584-
{
585-
schism_var->set_horizontal_center((att_var->as_string(0)));
586-
}
587-
else if (!(nc_att_name.compare(MeshConstants10::LAYER_CENTER)))
633+
//if ((!(nc_att_name.compare(MeshConstants10::CENTER)))||(!(nc_att_name.compare(MeshConstants10::LOCATION))))
634+
//{
635+
// schism_var->set_horizontal_center((att_var->as_string(0)));
636+
//}
637+
//else if (!(nc_att_name.compare(MeshConstants10::LAYER_CENTER)))
638+
//{
639+
// schism_var->set_vertical_center(att_var->as_string(0));
640+
//}
641+
642+
if (!(nc_att_name.compare(MeshConstants10::I23D)))
588643
{
589-
schism_var->set_vertical_center(att_var->as_string(0));
644+
int i23d = att_var->as_int(0);
645+
if (i23d <= 3)
646+
{
647+
schism_var->set_horizontal_center(MeshConstants10::NODE);
648+
}
649+
else if (i23d <= 6)
650+
{
651+
schism_var->set_horizontal_center(MeshConstants10::ELEM);
652+
}
653+
else if (i23d <= 9)
654+
{
655+
schism_var->set_horizontal_center(MeshConstants10::EDGE);
656+
}
657+
else
658+
{
659+
throw SCHISMVarException10("i23d is not a valid\n");
660+
}
661+
662+
if (!(i23d % 3))
663+
{
664+
schism_var->set_vertical_center(MeshConstants10::HALF_LAYER);
665+
}
666+
else
667+
{
668+
schism_var->set_vertical_center(MeshConstants10::FULL_LAYER);
669+
}
590670
}
591671

592672
}
@@ -652,7 +732,14 @@ void MDSchismOutputVar::fill_ncVar(NcVar * a_nc_var)
652732
}
653733
else
654734
{
655-
m_schismfilePtr->get_face_bottom(a_kbp00,m_current_record);
735+
if (m_vertical_center == MeshConstants10::HALF_LAYER)
736+
{
737+
m_schismfilePtr->get_prism_bottom(a_kbp00, m_current_record);
738+
}
739+
else
740+
{
741+
m_schismfilePtr->get_face_bottom(a_kbp00, m_current_record);
742+
}
656743
}
657744
}
658745

@@ -685,7 +772,7 @@ bool MDSchismOutputVar::get(int * a_buffer)
685772
{
686773

687774
int dataSize = computeDataNumPerTIMEStep();
688-
debug1 << "data size is " << dataSize<<"\n";
775+
//debug1 << "data size is " << dataSize<<"\n";
689776
if(m_data_cached)
690777
{
691778
//for(int idata=0;idata<dataSize;idata++)

‎mdschism/MDSCHISMOutput.h‎

Lines changed: 14 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
#include "SCHISMFile10.h"
22
#include "MeshConstants10.h"
33
#include "netcdfcpp.h"
4-
#include <DebugStream.h>
4+
//#include <DebugStream.h>
55
#ifndef _MDNETCDFSCHISMOUTPUT_H_
66
#define _MDNETCDFSCHISMOUTPUT_H_
77

@@ -19,6 +19,8 @@ class MDSchismOutput: public SCHISMFile10
1919
void get_node_bottom(int* a_node_bottom,const int& a_time);
2020
void get_face_bottom(int* a_face_bottom,const int& a_time);
2121
void get_edge_bottom(int* a_ele_bottom,const int& a_time);
22+
void get_prism_bottom(int* a_prism_bottom, const int& a_time);
23+
void set_prism_bottom(const int& a_time, int* a_prism_bottom);
2224
bool update_bottom_index(const int& a_time);
2325
int global_att_as_int(const std::string& a_att_name) const;
2426
std::string global_att_as_string(const std::string& a_att_name) const;
@@ -37,7 +39,7 @@ class MDSchismOutput: public SCHISMFile10
3739
bool update_node_bottom(const int& a_time);
3840
void update_edge_bottom(const int& a_time, int* a_node_bottom);
3941
void update_ele_bottom(const int& a_time,int* a_node_bottom);
40-
42+
void update_prism_bottom(const int& a_time, int* a_prism_bottom);
4143

4244

4345
NcFile* m_outputNcFilePtr;
@@ -49,9 +51,11 @@ class MDSchismOutput: public SCHISMFile10
4951
int* m_face_bottom;
5052
int* m_node_bottom;
5153
int* m_edge_bottom;
54+
int* m_prism_bottom;
5255
int m_face_bottom_time_id;
5356
int m_node_bottom_time_id;
5457
int m_edge_bottom_time_id;
58+
int m_prism_bottom_time_id;
5559
long * m_face_nodes;
5660
long * m_side_nodes;
5761
};
@@ -124,7 +128,7 @@ bool MDSchismOutputVar::load_from_file(T * a_buffer)
124128
int num_dim = ncvar->num_dims();
125129
long * current = new long [num_dim];
126130
long * count = new long [num_dim];
127-
debug1 << " begin load dims in load from file\n";
131+
//debug1 << " begin load dims in load from file\n";
128132
for(int idim =0; idim<num_dim;idim++)
129133
{
130134
// int dim_id = m_dimensions[idim];
@@ -153,7 +157,7 @@ bool MDSchismOutputVar::load_from_file(T * a_buffer)
153157
}
154158
}
155159

156-
//debug1 << " done load dims in load from file\n";
160+
//debug1 << " done load dims in load from file "<<buffer_size<<" "<<node_num<<" "<<num_layer<<"\n";
157161
if (num_layer ==1) // not 3d data
158162
{
159163

@@ -197,7 +201,7 @@ bool MDSchismOutputVar::load_from_file(T * a_buffer)
197201
int * bottom_layer = new int [node_num];
198202

199203
fill_current_bottom(bottom_layer);
200-
204+
201205
long * start_loc = new long [node_num];
202206

203207
for(long inode=0;inode<node_num;inode++)
@@ -253,9 +257,9 @@ bool MDSchismOutputVar::load_from_file(T * a_buffer)
253257
ncvar->get(buffer,count);
254258
}
255259

256-
260+
//debug1 << "done read ncvar data\n";
257261
int a_node_record_length_in_nc_buffer = buffer_size/node_num;
258-
262+
long total_valid_data_len = 0;
259263
for(long inode=0;inode<node_num;inode++)
260264
{
261265
long a_node_valid_data_start= start_loc[inode];
@@ -278,8 +282,10 @@ bool MDSchismOutputVar::load_from_file(T * a_buffer)
278282
a_buffer[valid_data_index] = buffer[nc_buffer_id];
279283
nc_buffer_id++;
280284
}
285+
//debug1 << "done read valid ncvar data "<<inode<<" " << valid_record_start_in_nc_buffer<<"\n";
286+
total_valid_data_len += a_node_valid_record_len;
281287
}
282-
288+
//debug1 << "done read valid ncvar data " <<total_valid_data_len<<"\n";
283289
delete buffer;
284290

285291

‎mdschism/MeshConstants10.h‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -61,6 +61,7 @@ const std::string LAYER_CENTER("data_vertical_center");
6161
const std::string FULL_LAYER("full");
6262
const std::string HALF_LAYER("half");
6363
const std::string DYNAMIC_MESH("mesh_is_dynamic");
64+
const std::string I23D("i23d");
6465
const float DRY_ZCOR=-99999999.0;
6566
const long INVALID_NUM = -9999;
6667
const int MAX_NUM_NODE_PER_CELL = 4;

‎mdschism/SCHISMFile10.cpp‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -624,7 +624,6 @@ bool SCHISMFile10::none_data_var(const std::string a_varName) const
624624
{
625625
return false;
626626
}
627-
628627
}
629628
std::string SCHISMFile10::file() const
630629
{
@@ -741,6 +740,10 @@ void SCHISMFile10::get_face_bottom(int* a_face_bottom,const int& a_time)
741740
return;
742741
}
743742

743+
void SCHISMFile10::get_prism_bottom(int* a_face_bottom, const int& a_time)
744+
{
745+
return;
746+
}
744747
void SCHISMFile10::get_edge_bottom(int* a_ele_bottom,const int& a_time)
745748
{
746749
return;

‎mdschism/SCHISMFile10.h‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -238,6 +238,7 @@ class SCHISMFile10
238238
virtual void get_node_bottom(int* a_node_bottom,const int& a_time);
239239
virtual void get_face_bottom(int* a_face_bottom,const int& a_time);
240240
virtual void get_edge_bottom(int* a_ele_bottom,const int& a_time);
241+
virtual void get_prism_bottom(int* a_ele_bottom, const int& a_time);
241242
virtual int global_att_as_int(const std::string& a_att_name) const;
242243
virtual std::string global_att_as_string(const std::string& a_att_name) const;
243244
private:

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