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Simplify SW_NC_write_output()
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- Remove functions `output_file()` & `get_start_dims()`
- Remove year calculations
- Correct the write dimension sizes for domain type "s"
	* `get_write_dim_sizes()` gains number of layers for the current output key
- New function `calc_pOUTIndex()`
	* Abstracts the calculation of the starting index of `p_OUT` from `SW_NC_write_output()`
- Get time size directly from the opened output file instead of calculating the location of the value within `dimSizes`
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@N1ckP3rsl3y
N1ckP3rsl3y committed Feb 5, 2024
1 parent f128579 commit a8e3dbf
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Showing 3 changed files with 58 additions and 92 deletions.
4 changes: 2 additions & 2 deletions include/SW_netCDF.h
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Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,8 @@ extern int numVarsPerKey[];
/* Global Function Declarations */
/* --------------------------------------------------- */
void SW_NC_write_output(SW_OUTPUT* SW_Output, SW_GEN_OUT* SW_GenOut,
int numFilesPerKey, char** ncOutFileNames[][SW_OUTNPERIODS],
size_t ncSuid[], int strideOutYears, int startYr, int endYr,
LyrIndex n_layers, int n_evap_layers, int numFilesPerKey,
char** ncOutFileNames[][SW_OUTNPERIODS], size_t ncSuid[],
LOG_INFO* LogInfo);
void SW_NC_create_output_files(const char* domFile, int domFileID,
SW_OUTPUT* SW_Output, int strideOutYears, int startYr, int endYr,
Expand Down
4 changes: 2 additions & 2 deletions src/SW_Control.c
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Original file line number Diff line number Diff line change
Expand Up @@ -800,9 +800,9 @@ void SW_CTL_run_sw(SW_ALL* sw_template, SW_DOMAIN* SW_Domain, unsigned long ncSu

#if defined(SWNETCDF)
SW_NC_write_output(local_sw.Output, &local_sw.GenOutput,
local_sw.Site.n_layers, local_sw.Site.n_evap_lyrs,
local_sw.FileStatus.numOutFiles, local_sw.FileStatus.ncOutFiles,
ncSuid, SW_Domain->netCDFInfo.strideOutYears,
local_sw.Model.startyr, local_sw.Model.endyr, LogInfo);
ncSuid, LogInfo);

full_reset = swTRUE;
#endif
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142 changes: 54 additions & 88 deletions src/SW_netCDF.c
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Original file line number Diff line number Diff line change
Expand Up @@ -966,27 +966,6 @@ static void init_output_var_info(SW_OUTPUT* SW_Output, LOG_INFO* LogInfo) {
}
}

/**
* @brief Determines if the netCDF output file is to be written to
* by checking if there were any requested output variables
*
* @param[in] SW_Output SW_OUTPUT array of size SW_OUTNKEYS which holds
* basic output information for all output keys
* @param[in] key Specifies what output key is currently being allocated
* (i.e., temperature, precipitation, etc.)
*/
static Bool output_file(SW_OUTPUT* SW_Output, OutKey key) {
int varNum;

for(varNum = 0; varNum < numVarsPerKey[key]; varNum++) {
if(SW_Output->reqOutputVars[varNum]) {
return swTRUE;
}
}

return swFALSE;
}

/**
* @brief Helper function to `fill_domain_netCDF_vars()` to allocate
* memory for writing out values
Expand Down Expand Up @@ -2312,7 +2291,7 @@ static void create_output_file(SW_OUTPUT* SW_Output,
const int nameAtt = 0;

int newFileID = -1; // Default to not created
int cellMethAttInd;
int cellMethAttInd = 0;
char* varName, *dimStr = NULL;
char** varInfo;

Expand Down Expand Up @@ -2370,27 +2349,6 @@ static void create_output_file(SW_OUTPUT* SW_Output,
}
}

/**
* @brief Determine the starting dimensions to write data to the current
* file
*
* @param[out] start Start indices that the netCDF function will use
* @param[in] ncSuid Unique indentifier of the current suid being simulated
* @param[in] ncFileID File identifier to gather any necessary information
* from
*/
static void get_start_dims(size_t start[], size_t ncSuid[], int ncFileID) {

int index;
Bool twoDimDom = (Bool) (dimExists("lon", ncFileID) ||
dimExists("x", ncFileID));
int additionDimStart = (twoDimDom) ? 2 : 1;

for(index = 0; index < MAX_NUM_DIMS; index++) {
start[index] = (index < additionDimStart) ? ncSuid[index] : 0;
}
}

/**
* @brief Determine the write dimensions/sizes for the current
* output variable/period
Expand All @@ -2402,16 +2360,16 @@ static void get_start_dims(size_t start[], size_t ncSuid[], int ncFileID) {
* @param[out] LogInfo Holds information on warnings and errors
*/
static void get_write_dim_sizes(int ncFileID, size_t dimSizes[], char* dimStr,
LOG_INFO* LogInfo) {
int n_layers, LOG_INFO* LogInfo) {

char* wkgDimPtr = dimStr, *dimName;
Bool twoDimDom = (Bool) (dimExists("lon", ncFileID) || dimExists("x", ncFileID));
char* wkgDimPtr = dimStr, *dimName = NULL;
Bool twoDimDom = !((Bool)dimExists("site", ncFileID));
Bool readDimVal;
int numDims = 0, index;

dimSizes[numDims] = 1;
dimSizes[numDims + 1] = twoDimDom ? 1 : 0;
numDims += 2;
dimSizes[numDims + 1] = (twoDimDom) ? 1 : 0;
numDims += (twoDimDom) ? 2 : 1;

while(*wkgDimPtr != '\0') {
readDimVal = swTRUE;
Expand All @@ -2424,17 +2382,19 @@ static void get_write_dim_sizes(int ncFileID, size_t dimSizes[], char* dimStr,
dimName = (char *)"pft";
break;
case 'Z':
dimName = (char *)"vertical";
dimSizes[numDims] = (size_t)n_layers;
break;
default:
readDimVal = swFALSE;
break;
}

if(readDimVal) {
get_dim_val(ncFileID, dimName, &dimSizes[numDims], LogInfo);
if(LogInfo->stopRun) {
return; // Exit function prematurely due to error
if(*wkgDimPtr != 'Z') {
get_dim_val(ncFileID, dimName, &dimSizes[numDims], LogInfo);
if(LogInfo->stopRun) {
return; // Exit function prematurely due to error
}
}

numDims++;
Expand All @@ -2447,6 +2407,32 @@ static void get_write_dim_sizes(int ncFileID, size_t dimSizes[], char* dimStr,
}
}

/**
* @brief Calculate the starting index that will be used to write from
* `p_OUT`
*
* @param[in] SW_GenOut Holds general variables that deal with output
* @param[in] ncFileID Identifier of the open netCDF file to check
* @param[in] varNum Variable number within the current key
* @param[in] pd Current output netCDF period
* @param[in] vertSize Size of "vertical" dimension (if any)
* @param[in] startTime Start number of days when dealing with
* years between netCDF files
*/
static int calc_pOUTIndex(SW_GEN_OUT* SW_GenOut, int ncFileID, int varNum,
OutPeriod pd, int vertSize, int startTime) {
int pOUTIndex = 0;

if(dimExists("vertical", ncFileID) && dimExists("pft", ncFileID)) {
pOUTIndex = iOUT2(varNum, 0, pd, (*SW_GenOut), vertSize);
} else {
pOUTIndex = iOUT(varNum, pd, (*SW_GenOut));
}
pOUTIndex += startTime;

return pOUTIndex;
}

/* =================================================== */
/* Global Function Definitions */
/* --------------------------------------------------- */
Expand All @@ -2458,55 +2444,41 @@ static void get_write_dim_sizes(int ncFileID, size_t dimSizes[], char* dimStr,
* @param[in] SW_Output SW_OUTPUT array of size SW_OUTNKEYS which holds
* basic output information for all output keys
* @param[in] SW_GenOut Holds general variables that deal with output
* @param[in] n_layers Number of layers to write out
* @param[in] n_evap_layers Number of layers in which evap is possible
* @param[in] numFilesPerKey Number of output netCDFs each output key will
* have (same amount for each key)
* @param[in] ncOutFileNames A list of the generated output netCDF file names
* @param[in] ncSuid Unique indentifier of the current suid being simulated
* @param[in] strideOutYears Number of years to write into an output file
* @param[in] startYr Start simulation year
* @param[in] endYr End simulation year
* @param[out] LogInfo Holds information on warnings and errors
*/
void SW_NC_write_output(SW_OUTPUT* SW_Output, SW_GEN_OUT* SW_GenOut,
int numFilesPerKey, char** ncOutFileNames[][SW_OUTNPERIODS],
size_t ncSuid[], int strideOutYears, int startYr, int endYr,
LyrIndex n_layers, int n_evap_layers, int numFilesPerKey,
char** ncOutFileNames[][SW_OUTNPERIODS], size_t ncSuid[],
LOG_INFO* LogInfo) {

OutKey key;
OutPeriod pd;
RealD *p_OUTValPtr = NULL;
int fileNum, numYears = endYr - startYr + 1;
int currFileID = 0, varNum;
int fileNum, currFileID = 0, varNum;

char* fileName, *varName, *dimStr = NULL;
size_t dimSizes[MAX_NUM_DIMS] = {0};
size_t start[] = {0, 0, 0, 0, 0};
int pOUTIndex, startTime, timeSize = 0;
int rangeStart, rangeEnd, timeIndMin, timeIndMax;

int yearOffset = (strideOutYears == 1) ? 1 :
(int) ceil((double) numYears / strideOutYears);
size_t pOUTIndex, startTime, timeSize = 0;
int vertSize;

ForEachOutPeriod(pd) {
rangeStart = startYr;

if(!SW_GenOut->use_OutPeriod[pd]) {
continue; // Skip period iteration
}

for(fileNum = 0; fileNum < numFilesPerKey; fileNum++) {
if(rangeStart + yearOffset > endYr) {
rangeEnd = rangeStart + (endYr - rangeStart) + 1;
} else {
rangeEnd = rangeStart + yearOffset;
}

ForEachOutKey(key) {
startTime = 0;
vertSize = getNLayers(key, n_layers, n_evap_layers);

if(numVarsPerKey[key] == 0 || !SW_Output[key].use ||
!output_file(&SW_Output[key], key)) {

if(numVarsPerKey[key] == 0 || !SW_Output[key].use) {
continue; // Skip key iteration
}
fileName = ncOutFileNames[key][pd][fileNum];
Expand All @@ -2526,17 +2498,17 @@ void SW_NC_write_output(SW_OUTPUT* SW_Output, SW_GEN_OUT* SW_GenOut,
varName = SW_Output[key].outputVarInfo[varNum][VARNAME_INDEX];
dimStr = SW_Output[key].outputVarInfo[varNum][DIM_INDEX];

pOUTIndex = SW_GenOut->nrow_OUT[pd];
pOUTIndex *= ncol_TimeOUT[pd] + varNum;
pOUTIndex += startTime;
pOUTIndex = calc_pOUTIndex(SW_GenOut, currFileID, varNum,
pd, vertSize, startTime);

get_write_dim_sizes(currFileID, dimSizes, dimStr,
LogInfo);
vertSize, LogInfo);
if(LogInfo->stopRun) {
return; // Exit function prematurely due to error
}

get_start_dims(start, ncSuid, currFileID);
start[0] = ncSuid[0];
start[1] = ncSuid[1];

p_OUTValPtr = &SW_GenOut->p_OUT[key][pd][pOUTIndex];

Expand All @@ -2546,14 +2518,8 @@ void SW_NC_write_output(SW_OUTPUT* SW_Output, SW_GEN_OUT* SW_GenOut,
return; // Exit function prematurely due to error
}
}
// Detect if the "vertical" dimension is before "time" dimension
timeIndMin = dimExists("site", currFileID) ? 1 : 2;
timeIndMax = dimExists("site", currFileID) ? 2 : 3;

timeSize = dimExists("vertical", currFileID) ?
dimSizes[timeIndMax] : dimSizes[timeIndMin];

rangeStart = rangeEnd;
// Get the time value from the "time" dimension
get_dim_val(currFileID, "time", &timeSize, LogInfo);
startTime += timeSize;

nc_close(currFileID);
Expand Down

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