#include <iostream>
#include <netcdf.h>
#include <string>
#include <chrono>
#include <ctime>
#include <iomanip>
#include <sstream>

#include "config.h"
#include "outputter.h"
#include "grid_cell.h"

using namespace std;
using namespace glm;

/******************************************************************************/
void Outputter::init (string baseFileName, int startYear,
                      double lat[], double lon[], Config& config) {

   now_ = 0;
   startYear_ = startYear;

   index_[0] = 0;
   index_[1] = 0;
   index_[2] = 0;

   count_[0] = NT;
   count_[1] = NY;
   count_[2] = NX;

   stateFile_ = new OutputFile(baseFileName+"states.nc", config);
   flowsFile_ = new OutputFile(baseFileName+"transitions.nc", config);
   mngmtFile_ = new OutputFile(baseFileName+"management.nc", config);
   diagnFile_ = new OutputFile(baseFileName+"diagnostics.nc", config);
   
   initVars(config);

   stateFile_->addLatLon(lat, lon);
   flowsFile_->addLatLon(lat, lon);
   mngmtFile_->addLatLon(lat, lon);
   diagnFile_->addLatLon(lat, lon);
}


/******************************************************************************/
Outputter::OutputFile::OutputFile(string fileName, Config& config) {

   int rv;
   if ((rv = nc_create(fileName.c_str(), NC_NETCDF4 | NC_CLASSIC_MODEL, &fileID_))) {
      NCERR(fileName.c_str(), rv);
   }
   
   if ((rv = nc_def_dim(fileID_, "time", NC_UNLIMITED, &timeDimID_))) {
      NCERR(fileName.c_str(), rv);
   }
   if ((rv = nc_def_dim(fileID_, "lat", NY, &latDimID_))) {
      NCERR(fileName.c_str(), rv);
   }
   if ((rv = nc_def_dim(fileID_, "lon", NX, &lonDimID_))) {
      NCERR(fileName.c_str(), rv);
   }

   // Time
   if ((rv = nc_def_var(fileID_, "time", NC_DOUBLE, 1, &timeDimID_, &timeVarID_))) {
      NCERR("time", rv);
   }   
   
   if (!config.futureRun){
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "units",
                             strlen("years since 850-01-01 0:0:0"), "years since 850-01-01 0:0:0"))) {
      NCERR("time", rv);
   }
   }
   else {
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "units",
                             strlen("years since 2015-01-01 0:0:0"), "years since 2015-01-01 0:0:0"))) {
      NCERR("time", rv);
   }
   }
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "calendar",
                             strlen("noleap"), "noleap"))) {
      NCERR("time", rv);
   }
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "realtopology",
                             strlen("linear"), "linear"))) {
      NCERR("time", rv);
   }
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "long_name",
                             strlen("time"), "time"))) {
      NCERR("time", rv);
   }
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "standard_name",
                             strlen("time"), "time"))) {
      NCERR("time", rv);
   }
   if ((rv = nc_put_att_text(fileID_, timeVarID_, "axis",
                             strlen("T"), "T"))) {
      NCERR("time", rv);
   }   
   // Latitude
   if ((rv = nc_def_var(fileID_, "lat", NC_DOUBLE, 1, &latDimID_, &latVarID_))) {
      NCERR("lat", rv);
   }
   if ((rv = nc_put_att_text(fileID_, latVarID_, "realtopology",
                             strlen("linear"), "linear"))) {
      NCERR("lat", rv);
   }
   if ((rv = nc_put_att_text(fileID_, latVarID_, "units",
                             strlen("degrees_north"), "degrees_north"))) {
      NCERR("lat", rv);
   }
   if ((rv = nc_put_att_text(fileID_, latVarID_, "long_name",
                             strlen("latitude"), "latitude"))) {
      NCERR("lat", rv);
   }
   if ((rv = nc_put_att_text(fileID_, latVarID_, "standard_name",
                             strlen("latitude"), "latitude"))) {
      NCERR("lat", rv);
   }
   if ((rv = nc_put_att_text(fileID_, latVarID_, "axis",
                             strlen("Y"), "Y"))) {
      NCERR("lat", rv);
   }   
   // Longitude
   if ((rv = nc_def_var(fileID_, "lon", NC_DOUBLE, 1, &lonDimID_, &lonVarID_))) {
      NCERR("lon", rv);
   }  
   if ((rv = nc_put_att_text(fileID_, lonVarID_, "realtopology",
                             strlen("circular"), "circular"))) {
      NCERR("lon", rv);
   }
   if ((rv = nc_put_att_text(fileID_, lonVarID_, "topology",
                             strlen("circular"), "circular"))) {
      NCERR("lon", rv);
   }
   
   double modulo_val = (double)360.;
   if ((rv = nc_put_att_double(fileID_, lonVarID_, "modulo",
                             NC_DOUBLE, 1, &modulo_val))) {
      NCERR("lon", rv);
   }
   if ((rv = nc_put_att_text(fileID_, lonVarID_, "units",
                             strlen("degrees_east"), "degrees_east"))) {
      NCERR("lon", rv);
   }
   if ((rv = nc_put_att_text(fileID_, lonVarID_, "long_name",
                             strlen("longitude"), "longitude"))) {
      NCERR("lon", rv);
   }
   if ((rv = nc_put_att_text(fileID_, lonVarID_, "standard_name",
                             strlen("longitude"), "longitude"))) {
      NCERR("lon", rv);
   }
   if ((rv = nc_put_att_text(fileID_, lonVarID_, "axis",
                             strlen("X"), "X"))) {
      NCERR("lon", rv);
   }
   // Global attributes
   std::time_t t = std::chrono::system_clock::to_time_t(std::chrono::system_clock::now());
   std::stringstream str_time;
   str_time << std::put_time(std::localtime(&t), "%FT%TZ");
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "host",
                             strlen("UMD College Park"), "UMD College Park"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "comment",
                             strlen("LUH2"), "LUH2"))) {
      NCERR("Global", rv);
   }
      if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "contact",
           strlen("gchurtt@umd.edu, lchini@umd.edu, steve.frolking@unh.edu, ritvik@umd.edu"), 
              "gchurtt@umd.edu, lchini@umd.edu, steve.frolking@unh.edu, ritvik@umd.edu"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "creation_date",
           strlen(str_time.str().c_str()), str_time.str().c_str()))) {
      NCERR("Global", rv);
   }
   
   
   if (!config.futureRun){
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "title",
           strlen("UofMD LUH2h dataset prepared for input4MIPs"), "UofMD LUH2h dataset prepared for input4MIPs"))) {
      NCERR("Global", rv);
   }
   }
   else{
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "title",
           strlen("UofMD LUH2f dataset prepared for input4MIPs"), "UofMD LUH2f dataset prepared for input4MIPs"))) {
      NCERR("Global", rv);
   }
   }
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "activity_id",
                             strlen("input4MIPs"), "input4MIPs"))) {
      NCERR("Global", rv);
   }   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "Conventions",
                             strlen("CF-1.6"), "CF-1.6"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "data_structure",
                             strlen("grid"), "grid"))) {
      NCERR("Global", rv);
   }
   if (!config.futureRun){
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "source",
                             strlen("LUH2 v2.1h: Land-Use Harmonization Data Set"), "LUH2 v2.1h: Land-Use Harmonization Data Set"))) {
      NCERR("Global", rv);
   }
   }
   else{
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "source",
                             strlen("LUH2 v2.1f: Land-Use Harmonization Data Set"), "LUH2 v2.1f: Land-Use Harmonization Data Set"))) {
      NCERR("Global", rv);
   }
   
   }
   
   if (!config.futureRun){
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "dataset_version_number",
                             strlen("2.1h"), "2.1h"))) {
      NCERR("Global", rv);
   }  
   }
   else {
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "dataset_version_number",
                             strlen("2.1f"), "2.1f"))) {
      NCERR("Global", rv);
   }
   }
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "dataset_category",
                             strlen("landState"), "landState"))) {
      NCERR("Global", rv);
   } 
   
   if (!config.futureRun){
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "source_id",
                             strlen("UofMD-landState-2-1-h"), "UofMD-landState-2-1-h"))) {
      NCERR("Global", rv);
   }  
   }
   else {
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "source_id",
                             strlen("UofMD-landState-2-1-f"), "UofMD-landState-2-1-f"))) {
      NCERR("Global", rv);
   }
   
   } 
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "variable_id",
                             strlen("multiple"), "multiple"))) {
      NCERR("Global", rv);
   }
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "target_mip",
                             strlen("CMIP"), "CMIP"))) {
      NCERR("Global", rv);
   }
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "grid_label",
                             strlen("gn"), "gn"))) {
      NCERR("Global", rv);
   }
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "mip_era",
                             strlen("CMIP6"), "CMIP6"))) {
      NCERR("Global", rv);
   } 
   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "license",
                             strlen("Land-Use Harmonization data produced by the University of Maryland is licensed under a Creative Commons Attribution \\\"Share Alike\\\" 4.0 International License (http://creativecommons.org/licenses/by/4.0/). 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."), "Land-Use Harmonization data produced by the University of Maryland is licensed under a Creative Commons Attribution \\\"Share Alike\\\" 4.0 International License (http://creativecommons.org/licenses/by/4.0/). 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."))) {
      NCERR("Global", rv);
   }   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "further_info_url",
                             strlen("http://luh.umd.edu"), "http://luh.umd.edu"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "frequency",
                             strlen("yr"), "yr"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "institution_id",
                             strlen("UofMD"), "UofMD"))) {
      NCERR("Global", rv);
   }   
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "institution",
                             strlen("University of Maryland (UofMD), College Park, MD 20742, USA"), 
           "University of Maryland (UofMD), College Park, MD 20742, USA"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "realm",
                             strlen("land"), "land"))) {
      NCERR("Global", rv);
   }
   if ((rv = nc_put_att_text(fileID_, NC_GLOBAL, "references",
                             strlen("Hurtt, Chini et al. 2011"), 
           "Hurtt, Chini et al. 2011"))) {
      NCERR("Global", rv);
   }   
}


/******************************************************************************/
void Outputter::OutputFile::addLatLon(double lat[], double lon[]) {
   int rv;

   if ((rv = nc_enddef(fileID_))) {
      NCERR("enddef", rv);
   }

   if ((rv = nc_put_var_double(fileID_, latVarID_, &lat[0]))) {
      NCERR("lat", rv);
   } 

   if ((rv = nc_put_var_double(fileID_, lonVarID_, &lon[0]))) {
      NCERR("lon", rv);
   } 
   
}


/******************************************************************************/
void Outputter::OutputFile::addYear(size_t index, int year) {
   // Add a single year into open netCDF dataset
   
   int rv;

   size_t loc[1] = { index };
   if ((rv = nc_put_var1_int(fileID_, timeDimID_, &loc[0], &year))) {
      NCERR("lat", rv);
   }
}


/******************************************************************************/
void Outputter::initVars(Config& config) {
   for (size_t lu=PRIMF; lu<N_SUB_LU_TYPES; ++lu) {
      registerVarByLandUse(stateFile_,
                           string(getSubLandUseName((sub_lu_types)lu)),
                           string("area_fraction"),
                           string(getSubLandUseLongName((sub_lu_types)lu)),
                           (sub_lu_types)lu, "1",
                           &GridCell::getStateForOutput, 1e20F);
   }

   registerVar(stateFile_, "secmb", "vegetation_carbon_content", "secondary mean biomass carbon density",
               "kg m-2", &GridCell::getSSMB, 1e20F);
   registerVar(stateFile_, "secma", "", "secondary mean age",
               "years", &GridCell::getSSMA, 1e20F);
   registerVar(diagnFile_, "RSLossRem", "", "remote sensing forest loss remaining","fraction", &GridCell::getRSLossRem, 1e20F);

   registerVar(diagnFile_, "gldis", "area_fraction", "potential biomass carbon", "1", &GridCell::getLdis, 1e20F);
   registerVar(diagnFile_, "gzdis", "area_fraction", "Z distance", "1", &GridCell::getZdis, 1e20F);
   registerVar(diagnFile_, "gpbio", "area_fraction", "L distance", "1", &GridCell::getPotBio, 1e20F);
   registerVar(diagnFile_, "gs2c_sc", "area_fraction", "transition from secondary to cropland for shifting cultivation", "1", &GridCell::getS2C_SC, 1e20F);
   registerVar(diagnFile_, "gv2c_sc", "area_fraction", "transition from primary to cropland for shifting cultivation", "1", &GridCell::getV2C_SC, 1e20F);
   registerVar(diagnFile_, "gc2s_sc", "area_fraction", "transition from cropland to secondary for shifting cultivation", "1", &GridCell::getC2S_SC, 1e20F);
   
   for (size_t from=PRIMF; from<N_SUB_LU_TYPES; ++from) {
      for (size_t to=SECDF; to<N_SUB_LU_TYPES; ++to) {
         // Ignore primf_to_secdf and primn_to_secdn transtions since they are covered under wood harvest
         if ((from == PRIMF && to == SECDF) || (from == PRIMN && to == SECDN)) {
            continue;
         }
         
         if (from != to) {
            registerFlowVar((sub_lu_types)from, (sub_lu_types)to, "1", "area_fraction",
                            &GridCell::getFlowForOutput, 1e20F);
         }
      }
   }

   registerVar(flowsFile_, "primf_harv", "area_fraction", "wood harvest area from primary vegetation on LUH2 potential forest land",
               "1", &GridCell::getVAH1, 1e20F);
   registerVar(flowsFile_, "primn_harv", "area_fraction", "wood harvest area from primary vegetation on LUH2 potential non-forest land",
               "1", &GridCell::getVAH2, 1e20F);
   registerVar(flowsFile_, "secmf_harv", "area_fraction", "wood harvest area from secondary mature vegetation on LUH2 potential forest land",
               "1", &GridCell::getSAH1, 1e20F);
   registerVar(flowsFile_, "secyf_harv", "area_fraction", "wood harvest area from secondary young vegetation on LUH2 potential forest land ",
               "1", &GridCell::getSAH2, 1e20F);
   registerVar(flowsFile_, "secnf_harv", "area_fraction", "wood harvest area from secondary vegetation on LUH2 potential non-forest land",
               "1", &GridCell::getSAH3, 1e20F);

   registerVar(flowsFile_, "primf_bioh", "vegetation_carbon_content", "wood harvest biomass carbon from primary vegetation on LUH2 potential forest land",
               "kg", &GridCell::getVBH1, 1e20F);
   registerVar(flowsFile_, "primn_bioh", "vegetation_carbon_content", "wood harvest biomass carbon from primary vegetation on LUH2 potential non-forest land",
               "kg", &GridCell::getVBH2, 1e20F);
   registerVar(flowsFile_, "secmf_bioh", "vegetation_carbon_content", "wood harvest biomass carbon from secondary mature vegetation on LUH2 potential forest land",
               "kg", &GridCell::getSBH1, 1e20F);
   registerVar(flowsFile_, "secyf_bioh", "vegetation_carbon_content", "wood harvest biomass carbon from secondary young vegetation on LUH2 potential forest land",
               "kg", &GridCell::getSBH2, 1e20F);
   registerVar(flowsFile_, "secnf_bioh", "vegetation_carbon_content", "wood harvest biomass carbon from secondary vegetation on LUH2 potential non-forest land",
               "kg", &GridCell::getSBH3, 1e20F);


   if (config.run_management == 1) {
     for (size_t lu=C3ANN; lu<=C3NFX; ++lu) {
        sub_lu_types lut = (sub_lu_types)lu;
        registerVarByLandUse(mngmtFile_, string("fertl_")+getSubLandUseName(lut), "",
                             string("fertilization rate for ")+getSubLandUseLongName(lut),
                             lut, "kg ha-1 yr-1 (crop season)",
                             &GridCell::getFertForOutput, 1e20F);

        registerVarByLandUse(mngmtFile_, string("irrig_")+getSubLandUseName(lut), "",
                             string("irrigated fraction of ")+getSubLandUseLongName(lut),
                             lut, "1",
                             &GridCell::getIrrigForOutput, 1e20F); 

        registerVarByLandUse(mngmtFile_, string("crpbf_")+getSubLandUseName(lut), "area_fraction",
                             string(getSubLandUseLongName(lut))+" fraction of crop type area grown as biofuels",
                             lut, "1", 
                             &GridCell::getCroplandBiofuelsForOutput, 1e20F); 
     }

     for (size_t lu=C3PER; lu<=C4PER; ++lu) {
        sub_lu_types lut = (sub_lu_types)lu;
        registerVarByLandUse(mngmtFile_, string("fharv_")+getSubLandUseName(lut), "vegetation_carbon_content",
                             string("fraction of ")+getSubLandUseLongName(lut)+" biomass carbon harvested annually",
                             (sub_lu_types)lu, "1", 
                             &GridCell::getBiomassHarvestForOutput, 1e20F); 
     }

     registerVar(mngmtFile_, "flood",  "area_fraction", "flooded fraction of C3 annual crop area (e.g. for paddy rice",
                 "1", &GridCell::getFlooded, 1e20F);

     registerVar(mngmtFile_, "rndwd",  "vegetation_carbon_content", "industrial roundwood fraction of wood harvest biomass carbon",
                 "1",
                 &GridCell::getRoundwoodFraction, 1e20F);
     registerVar(mngmtFile_, "fulwd",  "vegetation_carbon_content", "fuelwood fraction of wood harvest biomass carbon",
                 "1",
                 &GridCell::getFuelwoodFraction, 1e20F);
     registerVar(mngmtFile_, "combf",  "vegetation_carbon_content", "commercial biofuels fraction of wood harvest biomass carbon",
                 "1",
                 &GridCell::getCommercialBiofuelFraction, 1e20F);
                 
      registerVar(mngmtFile_, "crpbf_total",  "area_fraction", "fraction of total cropland area area grown as 2nd generation biofuels",
                 "1",
                 &GridCell::getTotalCropBiofuel, 1e20F);

   }
}


/******************************************************************************/
template <class T>
void Outputter::VarTemplateBase<T>::createFileVar (OutputFile* file) {
   int rv;
   int dims[3] = { file->timeDimID_, file->latDimID_, file->lonDimID_ };

   if (typeid(T) == typeid(float)) {
      float fill = (float)fill_;
      if ((rv = nc_def_var(file->fileID_, name_.c_str(), NC_FLOAT, 3,
                           dims, &varID_))) {
         NCERR(name_.c_str(), rv);
      }
      if ((rv = nc_put_att_float(file->fileID_, varID_,
                                 "missing_value", NC_FLOAT, 1, &fill))) {
         NCERR(name_.c_str(), rv);
      }
      if ((rv = nc_put_att_float(file->fileID_, varID_,
                                 "_Fillvalue", NC_FLOAT, 1, &fill))) {
         NCERR(name_.c_str(), rv);
      }
   } else if (typeid(T) == typeid(int)) {
      int fill = (int)fill_;
      if ((rv = nc_def_var(file->fileID_, name_.c_str(), NC_INT, 3,
                           dims, &varID_))) {
         NCERR(name_.c_str(), rv);
      }
      if ((rv = nc_put_att_int(file->fileID_, varID_,
                               "missing_value", NC_INT, 1, &fill))) {
         NCERR(name_.c_str(), rv);
      }
      if ((rv = nc_put_att_int(file->fileID_, varID_,
                                 "_Fillvalue", NC_INT, 1, &fill))) {
         NCERR(name_.c_str(), rv);
      }
   }  else if (typeid(T) == typeid(double)) {
      double fill = (double)fill_;
      if ((rv = nc_def_var(file->fileID_, name_.c_str(), NC_DOUBLE, 3,
                           dims, &varID_))) {
         NCERR(name_.c_str(), rv);
      }
      if ((rv = nc_put_att_double(file->fileID_, varID_,
                               "missing_value", NC_DOUBLE, 1, &fill))) {
         NCERR(name_.c_str(), rv);
      }
      if ((rv = nc_put_att_double(file->fileID_, varID_,
                                 "_Fillvalue", NC_DOUBLE, 1, &fill))) {
         NCERR(name_.c_str(), rv);
      }
   } else {
      cerr << "unimplemented datatype for output var " << name_ << endl;
      exit(1);
   }

   if ((rv = nc_put_att_text(file->fileID_, varID_, "standard_name",
                             standardName_.length(), standardName_.c_str()))) {
      NCERR(standardName_.c_str(), rv);
   }
   
   if ((rv = nc_put_att_text(file->fileID_, varID_, "long_name",
                             longName_.length(), longName_.c_str()))) {
      NCERR(longName_.c_str(), rv);
   }

   if (!units_.empty()) {
      if ((rv = nc_put_att_text(file->fileID_, varID_, "units",
                                units_.length(), units_.c_str()))) {
         NCERR(name_.c_str(), rv);
      }
   }
   if ((rv = nc_put_att_text(fileID_, varID_, "cell_methods",
                             strlen("time:mean"), "time:mean"))) {
      NCERR("Global", rv);
   }
   
   nc_def_var_deflate(file->fileID_, varID_, 0, 1, 1);
}


/******************************************************************************/
void Outputter::updateOutputs (GridCell& gc, size_t gcNow) {
   vector<VarBase *>::iterator v;
   for (v=registeredVars_.begin(); v!=registeredVars_.end(); ++v) {
      (*v)->updateVal(now_, gc, gcNow);
   }
}


/******************************************************************************/
void Outputter::flush (bool writeFlows) {
   vector<VarBase *>::iterator v;

   // Add a single year into open netCDF dataset
   stateFile_->addYear(index_[0], startYear_ + index_[0]);
   if (writeFlows) {
      flowsFile_->addYear(index_[0], startYear_ + index_[0]);
   }
   mngmtFile_->addYear(index_[0], startYear_ + index_[0]);
   diagnFile_->addYear(index_[0], startYear_ + index_[0]);

   for (v=registeredVars_.begin(); v!=registeredVars_.end(); ++v) {
      // don't write flows if we don't want them (ie final year)
      if (writeFlows || flowsFile_->fileID_ != (*v)->fileID_) {
         (*v)->flush(index_, count_);
      }
   }

   // Synchronize the disk copy of a netCDF dataset with in-memory buffers.
   // From: https://www.unidata.ucar.edu/software/netcdf/netcdf-4/newdocs/netcdf-c/nc_005fsync.html
   // There are two reasons you might want to synchronize after writes:
   // To minimize data loss in case of abnormal termination, or
   // to make data available to other processes for reading immediately after it is written.
   stateFile_->sync();
   flowsFile_->sync();
   mngmtFile_->sync();
   diagnFile_->sync();

   index_[0]++;
}