CMOR user input

Click to expand JSON file
{
    "#note":           "explanation of what source_type is goes here",
    "source_type":            "AOGCM ISM AER",
 
    "#note":                  "CMIP6 valid experiment_ids are found in CMIP6_CV.json",
    "experiment_id":          "piControl-withism",
    "activity_id":            "ISMIP6",
    "sub_experiment_id":      "none",
 
    "realization_index":      "3",
    "initialization_index":   "1",
    "physics_index":          "1",
    "forcing_index":          "1",
 
    "#note":                  "Text stored in attribute variant_info (recommended, not required description of run variant)",
    "run_variant":            "3rd realization",
 
    "parent_experiment_id":   "historical",
    "parent_activity_id":     "CMIP",
    "parent_source_id":       "PCMDI-test-1-0",
    "parent_variant_label":   "r3i1p1f1",
 
    "parent_time_units":      "days since 1850-01-01",
    "branch_method":          "standard",
    "branch_time_in_child":   59400.0,
    "branch_time_in_parent":  59400.0,
 
    "#note":                  "institution_id must be registered at https://github.com/WCRP-CMIP/CMIP6_CVs/issues/new ",
    "institution_id":         "PCMDI",
 
    "#note":                  "source_id (model name) must be registered at https://github.com/WCRP-CMIP/CMIP6_CVs/issues/new ",
    "source_id":              "PCMDI-test-1-0",
 
    "calendar":               "360_day",
 
    "grid":                   "native atmosphere regular grid (3x4 latxlon)",
    "grid_label":             "gn",
    "nominal_resolution":     "10000 km",
 
    "license":                 "CMIP6 model data produced by Lawrence Livermore PCMDI is licensed under a Creative Commons Attribution ShareAlike 4.0 International License (https://creativecommons.org/licenses). Consult https://pcmdi.llnl.gov/CMIP6/TermsOfUse for terms of use governing CMIP6 output, including citation requirements and proper acknowledgment. Further information about this data, including some limitations, can be found via the further_info_url (recorded as a global attribute in this file) and at https:///pcmdi.llnl.gov/. The data producers and data providers make no warranty, either express or implied, including, but not limited to, warranties of merchantability and fitness for a particular purpose. All liabilities arising from the supply of the information (including any liability arising in negligence) are excluded to the fullest extent permitted by law.",
 
    "#output":                "Root directory for output (can be either a relative or full path)",
    "outpath":                "CMIP6",
 
    "#note":                  " **** The following descriptors are optional and may be set to an empty string ",  
 
    "contact ":               "Python Coder (coder@a.b.c.com)",
    "history":                "Output from archivcl_A1.nce/giccm_03_std_2xCO2_2256.",
    "comment":                "",
    "references":             "Model described by Koder and Tolkien (J. Geophys. Res., 2001, 576-591).  Also see http://www.GICC.su/giccm/doc/index.html.  The ssp245 simulation is described in Dorkey et al. '(Clim. Dyn., 2003, 323-357.)'",
 
    "#note":                  " **** The following will be obtained from the CV and do not need to be defined here", 
 
    "sub_experiment":         "none",
    "institution":            "",
    "source":                 "PCMDI-test 1.0 (1989)",
 
    "#note":                  " **** The following are set correctly for CMIP6 and should not normally need editing",  
 
    "_control_vocabulary_file": "CMIP6_CV.json",
    "_AXIS_ENTRY_FILE":         "CMIP6_coordinate.json",
    "_FORMULA_VAR_FILE":        "CMIP6_formula_terms.json",
    "_cmip6_option":           "CMIP6",
 
    "mip_era":                "CMIP6",
    "parent_mip_era":         "CMIP6",
 
    "tracking_prefix":        "hdl:21.14100",
    "_history_template":       "%s ;rewrote data to be consistent with <activity_id> for variable <variable_id> found in table <table_id>.",
 
    "#output_path_template":   "Template for output path directory using tables keys or global attributes, these should follow the relevant data reference syntax",
    "output_path_template":    "<mip_era><activity_id><institution_id><source_id><experiment_id><_member_id><table><variable_id><grid_label><version>",
    "output_file_template":    "<variable_id><table><source_id><experiment_id><_member_id><grid_label>",
}



C source code

Click to expand C code
#include <time.h>
#include <stdio.h>
#include<string.h>
#include "cmor.h"
#include <stdlib.h>

void read_coords(alats, alons, plevs, bnds_lat, bnds_lon, lon, lat, lev)
double *alats, *alons;
int *plevs;
double *bnds_lat, *bnds_lon;
int lon, lat, lev;
{
    int i;

    for (i = 0; i < lon; i++) {
        alons[i] = i * 360. / lon;
        bnds_lon[2 * i] = (i - 0.5) * 360. / lon;
        bnds_lon[2 * i + 1] = (i + 0.5) * 360. / lon;
    };

    for (i = 0; i < lat; i++) {
        alats[i] = (lat - i) * 10;
        bnds_lat[2 * i] = (lat - i) * 10 + 5.;
        bnds_lat[2 * i + 1] = (lat - i) * 10 - 5.;
    };

    plevs[0] = 1000;
    plevs[1] = 925;
    plevs[2] = 850;
    plevs[3] = 700;
    plevs[4] = 600;
    plevs[5] = 500;
    plevs[6] = 400;
    plevs[7] = 300;
    plevs[8] = 250;
    plevs[9] = 200;
    plevs[10] = 150;
    plevs[11] = 100;
    plevs[12] = 70;
    plevs[13] = 50;
    plevs[14] = 30;
    plevs[15] = 20;
    plevs[16] = 10;
    plevs[17] = 5;
    plevs[18] = 1;
}

void read_time(it, time, time_bnds)
int it;
double time[];
double time_bnds[];
{
    time[0] = (it - 0.5) * 30.;
    time_bnds[0] = (it - 1) * 30.;
    time_bnds[1] = it * 30.;

    time[0] = it;
    time_bnds[0] = it;
    time_bnds[1] = it + 1;

}

#include "reader_2D_3D.h"

int main()
/*   Purpose:   To serve as a generic example of an application that */
/*       uses the "Climate Model Output Rewriter" (CMOR) */
/*    CMOR writes CF-compliant netCDF files. */
/*    Its use is strongly encouraged by the IPCC and is intended for use  */
/*       by those participating in many community-coordinated standard  */
/*       climate model experiments (e.g., AMIP, CMIP, CFMIP, PMIP, APE, */
/*       etc.) */
/*   Background information for this sample code: */
/*      Atmospheric standard output requested by IPCC are listed in  */
/*   tables available on the web.  Monthly mean output is found in */
/*   tables A1a and A1c.  This sample code processes only two 3-d  */
/*   variables listed in table A1c ("monthly mean atmosphere 3-D data"  */
/*   and only four 2-d variables listed in table A1a ("monthly mean  */
/*   atmosphere + land surface 2-D (latitude, longitude) data").  The  */
/*   extension to many more fields is trivial. */
/*      For this example, the user must fill in the sections of code that  */
/*   extract the 3-d and 2-d fields from his monthly mean "history"  */
/*   files (which usually contain many variables but only a single time  */
/*   slice).  The CMOR code will write each field in a separate file, but  */
/*   many monthly mean time-samples will be stored together.  These  */
/*   constraints partially determine the structure of the code. */
/*   Record of revisions: */
/*       Date        Programmer(s)           Description of change */
/*       ====        ==========              ===================== */
/*      10/22/03     Rusty Koder              Original code */
/*       1/28/04     Les R. Koder             Revised to be consistent */
/*                                            with evolving code design */
{
    /* --------------------------------- */
    /*   dimension parameters: */
    /* --------------------------------- */
#define   ntimes  2             /* number of time samples to process */
#define   lon  4                /* number of longitude grid cells   */
#define   lat  3                /* number of latitude grid cells */
#define   lev  19               /* number of standard pressure levels */
#define   n2d  4                /* number of IPCC Table A1a fields to be output. */
#define   n3d 3                 /* number of IPCC Table A1c fields to be output. */

    /*   Tables associating the user's variables with IPCC standard output  */
    /*   variables.  The user may choose to make this association in a  */
    /*   different way (e.g., by defining values of pointers that allow him  */
    /*   to directly retrieve data from a data record containing many  */
    /*   different variables), but in some way the user will need to map his  */
    /*   model output onto the Tables specifying the MIP standard output. */

    /* ---------------------------------- */

    /* My variable names for IPCC Table A1c fields */
    char varin3d[n3d][6] = { "CLOUD", "U", "T" };

    /* Units appropriate to my data */
    char units3d[n3d][6] = { "%", "m s-1", "K" };

    /* Corresponding IPCC Table A1c entry (variable name)  */
    char entry3d[n3d][3] = { "cl", "ua", "ta" };

    /* My variable names for IPCC Table A1a fields */
    char varin2d[n2d][9] = { "LATENT", "TSURF", "SOIL_WET", "PSURF" };

    /* Units appropriate to my data */
    char units2d[n2d][7] = { "W m-2", "K", "kg m-2", "Pa" };

    char positive2d[n2d][4] = { "down", " ", " ", " " };

    /* Corresponding IPCC Table A1a entry (variable name)  */
    char entry2d[n2d][6] = { "hfls", "tas", "mrsos", "ps" };

/*  uninitialized variables used in communicating with CMOR: */
/*  --------------------------------------------------------- */

    int error_flag;
    int znondim_id, zfactor_id;
    int var2d_ids[n2d];
    int var3d_ids[n3d];
    double data2d[lat * lon];
    double data3d[lev * lat * lon];
    double alats[lat];
    double alons[lon];
    int ilats[lat];
    int ilons[lon];
    double plevs[lev];
    int iplevs[lev];
    long lplevs[lev];
    float fplevs[lev];
    double Time[2];
    double bnds_time[4];
    double bnds_lat[lat * 2];
    double bnds_lon[lon * 2];
    double zlevs[lev];
    double zlev_bnds[lev + 1];

    double a_coeff[lev] = { 0.1, 0.2, 0.3, 0.22, 0.1 };
    double b_coeff[lev] = { 0.0, 0.1, 0.2, 0.5, 0.8 };
    float p0 = 1.e5;
    double a_coeff_bnds[lev + 1] = { 0., .15, .25, .25, .16, 0. };
    double b_coeff_bnds[lev + 1] = { 0., .05, .15, .35, .65, 1. };
    int ilon, ilat, ipres, ilev, itim;
    double dtmp, dtmp2;

    /*  Other variables: */
    /*  --------------------- */

    int it, m, i, ierr, j;
    int myaxes[10];
    int myaxes2[10];
    int myvars[10];
    char id[CMOR_MAX_STRING];
    char units[CMOR_MAX_STRING];
    char interval[CMOR_MAX_STRING];
    char anames[25][CMOR_MAX_STRING];
    char type;
    char regions[5][23] =
      { "atlantic_arctic_ocean", "indian_pacific_ocean", "pacific_ocean",
        "global_ocean", "sf_bay"
    };
    double timestest[5];
    /* Externals funcs */
    int tables[5];
    char msg[555];
    double bt = 0.;
    /* ================================ */
    /*  Execution begins here: */
    /* ================================ */

    /* Read coordinate information from model into arrays that will be passed  */
    /*   to CMOR. */
    /* Read latitude, longitude, and pressure coordinate values into  */
    /*   alats, alons, and plevs, respectively.  Also generate latitude and  */
    /*   longitude bounds, and store in bnds_lat and bnds_lon, respectively. */
    /*   Note that all variable names in this code can be freely chosen by */
    /*   the user. */

    /*   The user must write the subroutine that fills the coordinate arrays  */
    /*   and their bounds with actual data.  The following line is simply a */
    /*   a place-holder for the user's code, which should replace it. */

    /*  *** possible user-written call *** */

    m = CMOR_EXIT_ON_MAJOR;
    j = CMOR_REPLACE_4;
    i = 1;
    it = 0;
    printf("ok mode is:%i\n", m);
    ierr = cmor_setup(NULL, &j, NULL, &m, NULL, &i);    //,"  ipcc_test.LOG  ");

    read_coords(&alats[0], &alons[0], &iplevs[0], &bnds_lat[0], &bnds_lon[0],
                lon, lat, lev);
    int tmpmo[12];
    printf("Test code: ok init cmor\n");
    char c1[CMOR_MAX_STRING];
    char c2[CMOR_MAX_STRING];
    strcpy(c1, "GICCM1(2002)\0");
    strcpy(c2, "Nat\0");

    printf("yep: %s, %s\n", c1, c2);
    ierr = cmor_dataset_json("Test/CMOR_input_example.json");

    printf("Test code: ok load cmor table(s)\n");
    ierr = cmor_load_table("Tables/CMIP6_Omon.json", &tables[0]);
    ierr = cmor_load_table("Tables/CMIP6_Amon.json", &tables[1]);

    strcpy(id, "time");
    strcpy(units, "months since 1980");
    strcpy(interval, "1 month");

    read_time(0, &Time[0], &bnds_time[0]);
    read_time(1, &Time[1], &bnds_time[2]);
    ierr =
      cmor_axis(&myaxes[0], id, units, ntimes, &Time[0], 'd', &bnds_time[0], 2,
                interval);

    strcpy(id, "latitude");
    strcpy(units, "degrees_north");
    strcpy(interval, "");
    ierr =
      cmor_axis(&myaxes[1], id, units, lat, &alats, 'd', &bnds_lat, 2,
                interval);

    strcpy(id, "longitude");
    strcpy(units, "degrees_east");
    ierr =
      cmor_axis(&myaxes[2], id, units, lon, &alons, 'd', &bnds_lon, 2,
                interval);

    strcpy(id, "plev19");
    strcpy(units, "hPa");
    ierr =
      cmor_axis(&myaxes[3], id, units, lev, &iplevs, 'i', NULL, 0, interval);

    zlevs[0] = 0.1;
    zlevs[1] = 0.3;
    zlevs[2] = 0.5;
    zlevs[3] = 0.72;
    zlevs[4] = 0.9;

    zlev_bnds[0] = 0.;
    zlev_bnds[1] = .2;
    zlev_bnds[2] = .42;
    zlev_bnds[3] = .62;
    zlev_bnds[4] = .8;
    zlev_bnds[5] = 1.;
/*   p0 = 1.e5; */
/*   a_coeff = { 0.1, 0.2, 0.3, 0.22, 0.1 }; */
/*   b_coeff = { 0.0, 0.1, 0.2, 0.5, 0.8 }; */

/*   a_coeff_bnds={0.,.15, .25, .25, .16, 0.}; */
/*   b_coeff_bnds={0.,.05, .15, .35, .65, 1.}; */

    ierr =
      cmor_axis(&myaxes[4], "standard_hybrid_sigma", "1", 5, &zlevs, 'd',
                &zlev_bnds, 1, interval);

    cmor_set_table(tables[0]);
    /* ok here we declare a "regions" axis */
    printf("Test code: defining axis region \n");
    ierr =
      cmor_axis(&myaxes[5], "basin", "", 4, &regions[0], 'c', NULL, 23,
                interval);

    printf("Test code: Redefining time/lat from O table\n");

    strcpy(id, "time");
    strcpy(units, "months since 1980");
    strcpy(interval, "1 month");
    read_time(0, &Time[0], &bnds_time[0]);
    read_time(1, &Time[1], &bnds_time[2]);
    ierr =
      cmor_axis(&myaxes[7], id, units, ntimes, &Time[0], 'd', &bnds_time[0], 2,
                interval);

    strcpy(id, "latitude");
    strcpy(units, "degrees_north");
    strcpy(interval, "");
    ierr =
      cmor_axis(&myaxes[8], id, units, lat, &alats, 'd', &bnds_lat, 2,
                interval);

    cmor_set_table(tables[1]);

    dtmp = -999;
    dtmp2 = 1.e-4;
    myaxes2[0] = myaxes[0];
    myaxes2[1] = myaxes[3];
    myaxes2[2] = myaxes[1];
    myaxes2[3] = myaxes[2];

    printf("Test code: defining variables from table 1, %s\n", positive2d[0]);
    ierr =
      cmor_variable(&myvars[0], entry2d[0], units2d[0], 3, myaxes, 'd', &dtmp,
                    &dtmp2, positive2d[0], varin2d[0], "no history",
                    "no future");
    ierr =
      cmor_variable(&myvars[1], entry3d[2], units3d[2], 4, myaxes2, 'd', NULL,
                    &dtmp2, NULL, varin3d[2], "no history", "no future");

    printf("Test code: definig tas\n");
    ierr =
      cmor_variable(&myvars[5], "tas", "K", 3, myaxes, 'd', NULL, &dtmp2, NULL,
                    "TS", "no history", "no future");

    myaxes2[1] = myaxes[4];
    ierr =
      cmor_variable(&myvars[2], entry3d[0], units3d[0], 4, myaxes2, 'd', NULL,
                    &dtmp2, NULL, varin3d[0], "no history", "no future");
    ierr =
      cmor_zfactor(&myvars[3], myaxes2[1], "p0", "Pa", 0, NULL, 'f', &p0, NULL);
    ierr =
      cmor_zfactor(&myvars[3], myaxes2[1], "b", "", 1, &myaxes2[1], 'd',
                   &b_coeff, &b_coeff_bnds);
    ierr =
      cmor_zfactor(&myvars[3], myaxes2[1], "a", "", 1, &myaxes2[1], 'd',
                   &a_coeff, &a_coeff_bnds);
/*   printf("defining ap\n"); */
/*   for(i=0;i<5;i++) {a_coeff[i]*=1.e3;printf("sending acoef: %i, %lf\n",i,a_coeff[i]);} */
/*   for(i=0;i<6;i++) {a_coeff_bnds[i]*=1.e5;printf("sending acoef: %i, %lf\n",i,a_coeff_bnds[i]);} */
/*   ierr = cmor_zfactor(&myvars[3],myaxes2[1],"ap","hPa",1,&myaxes2[1],'d',&a_coeff,&a_coeff_bnds); */
    ierr =
      cmor_zfactor(&myvars[3], myaxes2[1], "ps", "hPa", 3, &myaxes[0], 'd',
                   NULL, NULL);

    /* ok here we decalre a variable for region axis testing */
    cmor_set_table(tables[0]);
    myaxes2[0] = myaxes[7];     /* time */
    myaxes2[1] = myaxes[5];     /* region */
    myaxes2[2] = myaxes[8];     /* latitudes */
    printf("Test code: ok we define hfogo positive: %s\n", positive2d[0]);
    ierr =
      cmor_variable(&myvars[4], "htovgyre", "W", 3, myaxes2, 'd', NULL, &dtmp2,
                    NULL, varin2d[0], "no history", "no future");

    cmor_set_table(tables[1]);

    for (i = 0; i < ntimes; i++) {
        printf("Test code: writing time: %i of %i\n", i + 1, ntimes);

        printf("2d\n");
        read_2d_input_files(i, varin2d[0], &data2d, lat, lon);
        sprintf(id, "%i", i);
        ierr = cmor_write(myvars[0], &data2d, 'd', NULL, 1, NULL, NULL, NULL);
        if (ierr)
            return (1);
        printf("3d\n");
        read_3d_input_files(i, varin3d[2], &data3d, lev, lat, lon);
        ierr = cmor_write(myvars[1], &data3d, 'd', NULL, 1, NULL, NULL, NULL);
        if (ierr)
            return (1);

        printf("writing tas\n");
        read_2d_input_files(i, varin2d[1], &data2d, lat, lon);
        ierr = cmor_write(myvars[5], &data2d, 'd', NULL, 1, NULL, NULL, NULL);
        if (ierr)
            return (1);

        printf("3d zfactor\n");
        read_3d_input_files(i, varin3d[0], &data3d, 5, lat, lon);
        ierr = cmor_write(myvars[2], &data3d, 'd', NULL, 1, NULL, NULL, NULL);
        if (ierr)
            return (1);

        printf("writing ps\n");
        read_2d_input_files(i, varin2d[3], &data2d, lat, lon);
        ierr = cmor_write(myvars[3], &data2d, 'd', NULL, 1, NULL, NULL, &myvars[2]);
        if (ierr)
            return (1);

        /* rereading hfls to fake hfogo */
        printf("2d region\n");
        read_2d_input_files(i, "htov", &data2d, lat, lon);
        ierr = cmor_write(myvars[4], &data2d, 'd', NULL, 1, NULL, NULL, NULL);
        if (ierr)
            return (1);

    }
    ierr = cmor_close_variable(myvars[0], NULL, NULL);
    ierr = cmor_close();
    return (0);
}

Tags: examples C