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Alomirdlebauer
Alomir
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dlebauer
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SIP80/SIP83 Remove multi-site support (#92)
* Removes code related to multi-site support * Updates for removal of multi-site support * Updates smoke test output * Updates tests after multi-site removal * Fixes example events.in * Adds test for *.param compatibility * Adds tests for param and clim compatibility, and fixes exposed bugs :-) * Fixes memory handling * Fixes lack of initialization for isRead * Updates CHANGELOG with more description of #92 effects * Adds check for '*' values in param file * remove references to multi-location runs from param file documentation * remove references to FILENAM.param-spatial from src/sipnet/sipnet.in * Updates comments in src/common/util.c Co-authored-by: David LeBauer <dlebauer@gmail.com> * Updates for PR feedback * Fixes sipnet moisture function restoration * Updates format for clang check * Adds note for new trim_first_chars utility --------- Co-authored-by: David LeBauer <dlebauer@gmail.com>
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‎Makefile‎

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@@ -1,13 +1,13 @@
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CC=gcc
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LD=gcc
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AR=ar -rs
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CFLAGS=-Wall -Werror -g -Isrc
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CFLAGS=-Wall -Werror -g -Isrc -Wno-c2x-extensions
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LIBLINKS=-lm
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LIB_DIR=./libs
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LDFLAGS=-L$(LIB_DIR)
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# Main executables
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COMMON_CFILES:=util.c namelistInput.c spatialParams.c
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COMMON_CFILES:=util.c namelistInput.c modelParams.c
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COMMON_CFILES:=$(addprefix src/common/, $(COMMON_CFILES))
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COMMON_OFILES=$(COMMON_CFILES:.c=.o)
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‎docs/CHANGELOG.md‎

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@@ -30,6 +30,7 @@ sections to include in release notes:
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- Changelog (#33)
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- Build docs and push to gh-pages (#41)
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- events.out file for agronomic event handling (#57)
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- utility `tools/trim_first_chars.sh` to trim the first n characters from every row in a file, useful for updating old input files to remove location column
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### Fixed
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@@ -40,12 +41,16 @@ sections to include in release notes:
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- Reorganized codebase (#34, #37)
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- Deprecated: "RUNTYPE" is obsolete. Will be silently ignored if set to 'standard' or error if set to anything else. Runs in 'standard' mode by default.
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- Deprecated: "LOCATION" is obsolete. Will be ignored with warning. (#92)
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- Deprecated: All columns in *.param except for name and value. Will be ignored with warning. (#92)
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- Deprecated: location column in input climate files. Will be ignored with warning. (#92)
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### Removed
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- Removed many experimental sites, data, and executable code as part of reorg (#34, #37)
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- Removed obsolete run types senstest and montecarlo and associated code (#69, #76)
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- Removed obsolete estimate program and associated code (#70, #82)
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- Removed multi-site support; in particular, output files no longer have a location column (#92)
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### Git SHA
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[TBD]
@@ -148,5 +153,3 @@ Braswell, Bobby H., William J. Sacks, Ernst Linder, and David S. Schimel. 2005.
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Sacks, William J., David S. Schimel, and Russell K. Monson. 2007. “Coupling between Carbon Cycling and Climate in a High-Elevation, Subalpine Forest: A Model-Data Fusion Analysis.” Oecologia 151 (1): 54–68. https://doi.org/10.1007/s00442-006-0565-2.
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Sacks, William J., David S. Schimel, Russell K. Monson, and Bobby H. Braswell. 2006. “Model‐data Synthesis of Diurnal and Seasonal CO2 Fluxes at Niwot Ridge, Colorado.” Global Change Biology 12 (2): 240–59. https://doi.org/10.1111/j.1365-2486.2005.01059.x.
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‎docs/parameters.md‎

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‎src/common/modelParams.c‎

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#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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#include <math.h>
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#include "exitCodes.h"
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#include "modelParams.h"
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#include "util.h"
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// Private/helper functions: not defined in modelParams.h
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// return 1 if all maxParams parameters have been initialized, 0 if not
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int allParamsInitialized(ModelParams *ModelParams) {
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if (ModelParams->numParams == ModelParams->maxParams) {
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// all parameters have been initialized
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return 1;
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}
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return 0;
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}
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// Set array[0..length-1] to all be equal to value
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void setAll(double *array, int length, double value) {
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int i;
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for (i = 0; i < length; i++) {
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array[i] = value;
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}
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}
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// Checks to make sure that all parameters with isRequired=true have been read
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// If not, kills program
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// Writes out names of all parameters that weren't read (even if not required,
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// as a warning message)
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void checkAllRead(ModelParams *ModelParams) {
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int i;
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int okay;
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OneModelParam *param;
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okay = 1; // so far so good
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for (i = 0; i < ModelParams->numParams; i++) {
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param = &(ModelParams->params[i]);
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if (param->value == NULL) {
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if (param->isRequired) { // should have been read but wasn't!
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okay = 0;
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printf("ERROR: Didn't read required parameter %s\n", param->name);
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} else {
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printf("WARNING: Didn't read parameter %s (not flagged as required, so "
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"continuing)\n",
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param->name);
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}
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}
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}
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if (!okay) {
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exit(1);
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}
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}
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/*************************************************/
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// Public functions: defined in ModelParams.h
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// allocate space for a new ModelParams structure, return a pointer to it
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ModelParams *newModelParams(int maxParams) {
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ModelParams *modelParams;
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modelParams = (ModelParams *)malloc(sizeof(ModelParams));
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modelParams->maxParams = maxParams;
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modelParams->numParams = 0; // for now, anyway
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modelParams->numParamsRead = 0; // for now, anyway
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// allocate space for vectors within this structure:
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modelParams->params =
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(OneModelParam *)malloc(maxParams * sizeof(OneModelParam));
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// Allocate enough space for reading all params
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modelParams->readIndices = (int *)malloc(maxParams * sizeof(int));
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return modelParams;
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}
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void initializeOneModelParam(ModelParams *modelParams, char *name,
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double *externalLoc, int isRequired) {
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int paramIndex; // index of next uninitialized parameter
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OneModelParam *param; // a pointer to the next uninitialized parameter
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if (allParamsInitialized(modelParams)) { // all parameters have been
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// initialized!
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printf("Error trying to initialize %s: have already initialized all %d "
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"parameters\n",
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name, modelParams->maxParams);
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printf("Check value of maxParams passed into newModelParams function\n");
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exit(1);
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}
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// otherwise, get the index of the next uninitialized parameter
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paramIndex = modelParams->numParams;
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// and set param to point to it for easier access
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param = &(modelParams->params[paramIndex]);
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strcpy(param->name, name);
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param->value = externalLoc;
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param->isRequired = isRequired;
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param->isRead = 0;
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modelParams->numParams++;
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}
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void checkParamFormat(char *line, const char *sep) {
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int numParams = countFields(line, sep);
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if (numParams > 2) {
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printf("WARNING: extra columns in .param file are being ignored (found %d "
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"columns)\n",
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numParams);
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}
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}
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void readModelParams(ModelParams *modelParams, FILE *paramFile) {
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const char *SEPARATORS = " \t\n\r"; // characters that can separate values in
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// parameter files
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const char *COMMENT_CHARS = "!"; // comment characters (ignore everything
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// after this on a line)
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char line[256];
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char pName[MODEL_PARAM_MAXNAME]; // parameter name
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int paramIndex;
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OneModelParam *param; // a pointer to a single parameter, for easier access
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char strValue[32]; // before we know whether value is a number or "*"
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double value;
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char *errc;
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int isComment;
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// Check for old-style (spatial param) format on first line containing params
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int formatChecked = 0;
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while (fgets(line, sizeof(line), paramFile) != NULL) { // while not EOF or
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// error
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// remove trailing comments:
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isComment = stripComment(line, COMMENT_CHARS);
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if (!isComment) { // if this isn't just a comment line or blank line
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// Check for old spatial-param format and warn if appropriate
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if (!formatChecked) {
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checkParamFormat(line, SEPARATORS);
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formatChecked = 1;
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}
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// tokenize line:
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strcpy(pName, strtok(line, SEPARATORS)); // copy first token into pName
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strcpy(strValue, strtok(NULL, SEPARATORS));
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if (strcmp(strValue, "*") == 0) {
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// This used to mean "spatially varying" when sipnet supported multiple
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// sites, but now this is an error
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printf("Error reading parameter %s; '*' is no longer supported\n",
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pName);
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exit(EXIT_CODE_BAD_PARAMETER_VALUE);
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}
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value = strtod(strValue, &errc);
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paramIndex = locateParam(modelParams, pName);
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if (paramIndex == -1) { // not found
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printf("WARNING: Ignoring parameter %s: this parameter wasn't "
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"initialized in the code\n",
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pName);
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} else if (valueSet(modelParams, paramIndex)) {
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printf("Error reading parameter file: read %s, but this parameter has "
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"already been set\n",
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pName);
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exit(EXIT_CODE_INPUT_FILE_ERROR);
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} else { // otherwise, we're good to go
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// set param to point to the appropriate parameter, for easier access
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param = &(modelParams->params[paramIndex]);
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*(param->value) = value;
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param->isRead = 1;
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// mark this as the next parameter read from file:
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modelParams->readIndices[modelParams->numParamsRead] = paramIndex;
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modelParams->numParamsRead++;
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} // else (no errors in reading this line from parameter file)
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} // if !isComment
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} // while not EOF or error
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// check for error in reading:
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if (ferror(paramFile)) {
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printf("Error reading file in readModelParams\n");
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printf("ferror = %d\n", ferror(paramFile));
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exit(1);
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}
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checkAllRead(modelParams); // terminate program if some required parameters
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// weren't read
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} // readModelParams
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// Return numParams, the actual number of parameters that have been
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// initialized with initializeOneModelParam
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int getnumParams(ModelParams *modelParams) { return modelParams->numParams; }
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// Return number of parameters that have been read in from file
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int getNumParamsRead(ModelParams *modelParams) {
200+
return modelParams->numParamsRead;
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}
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// Find parameter with given name in the parameters vector
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// If found, return index in vector, otherwise return -1
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int locateParam(ModelParams *modelParams, char *name) {
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int i;
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int found;
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i = 0;
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found = 0;
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while (i < modelParams->numParams && !found) {
212+
if (strcmpIgnoreCase(name, modelParams->params[i].name) == 0) {
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found = 1;
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}
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i++;
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}
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if (found) {
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return (i - 1);
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}
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return -1;
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}
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// Return 1 if parameter i has had its value set, 0 otherwise
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int valueSet(ModelParams *modelParams, int i) {
227+
return modelParams->params[i].isRead;
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}
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void deleteModelParams(ModelParams *modelParams) {
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// Free space used by ModelParams structure itself:
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free(modelParams->params);
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free(modelParams->readIndices);
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free(modelParams);
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}

‎src/common/modelParams.h‎

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#ifndef MODEL_PARAMS_H
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#define MODEL_PARAMS_H
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#include <stdio.h>
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#define MODEL_PARAM_MAXNAME 64
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// struct to hold a single param
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typedef struct OneModelParamStruct {
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char name[MODEL_PARAM_MAXNAME]; // name of parameter
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int isRequired; // 0 or 1; 1 indicates that we should terminate run if this
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// parameter isn't specified in input file
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double *value; // a pointer to this param's (external location) value
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int isRead; // whether this param has been read
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} OneModelParam;
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typedef struct ModelParamsStruct {
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OneModelParam *params; // vector of parameters, dynamically-allocated
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// (stored in order in which they were initialized)
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int maxParams; // maximum number of parameters
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int numParams; // actual number of parameters (tracks # that have been
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// initialized with initializeOneSpatialParam)
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int numParamsRead; // tracks number of parameters that have been read in from
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// file
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int *readIndices; // indices (in parameters vector) of the parameters read
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// from file, in the order in which they were read (this
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// will allow us to output parameters in the same order
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// later)
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} ModelParams;
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// allocate space for a new spatialParams structure, return a pointer to it
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ModelParams *newModelParams(int maxParameters);
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/* Initialize next parameter:
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Set name of parameter equal to "name",
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and set parameter's value pointer to point to the location given by
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"externalLoc" parameter (required to be non-NULL)
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Also set parameter's isRequired value: if true, then we'll terminate
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execution if this parameter is not read from file
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*/
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void initializeOneModelParam(ModelParams *params, char *name,
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double *externalLoc, int isRequired);
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/* Read all parameters from file, setting all values in Params structure
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appropriately
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Structure of paramFile:
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name value
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The order of the parameters in paramFile does not matter.
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! is a comment character in paramFile: anything after a ! on a line is
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ignored
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PRE: paramFile is open and file pointer points to start of file
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NOTE: for compatibility with the prior format, the following structure is
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also acceptable: name value changeable min max sigma When encountered,
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the extra columns are ignored and a warning is generated.
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*/
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void readModelParams(ModelParams *params, FILE *paramFile);
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// Return numParameters, the actual number of parameters that have been
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// initialized with initializeOneSpatialParam
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int getNumModelParams(ModelParams *params);
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// Return number of parameters that have been read in from file
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int getNumModelParamsRead(ModelParams *params);
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// Find parameter with given name in the parameters vector
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// If found, return index in vector, otherwise return -1
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int locateParam(ModelParams *params, char *name);
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// Return 1 if parameter i has had its value set, 0 otherwise
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int valueSet(ModelParams *params, int i);
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/* Check to see whether value is within allowable range of parameter i
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Return 1 if okay, 0 if bad
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*/
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int checkParam(ModelParams *params, int i, double value);
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/* Return value of parameter i
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PRE: 0 <= i < modelParams->numParameters
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*/
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double getParam(ModelParams *params, int i);
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// Clean up: deallocate modelParams and any other dynamically-allocated
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// pointers that need deallocating
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void deleteModelParams(ModelParams *params);
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#endif

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