SGP/PGS/C1 - Reprocessing User Notes

Time Variables - to make the PGS system more consistent with LBNL's other data streams, 
the variable 'yyyymmddhhmmss' was renamed 'yyyydddhhmmss'. Also, at the bottom of each 
file, variables 'yyyy','mon','hour','min' were added for those users who prefer to use these 
variables instead. The new 'time' variable (seconds since midnight of the start of file) 
was added to make files compatible with the new recommendations.

Quality Control Flags - to prevent confusion, the quality control flags 'qc_co2ppm' and 
'qc_sum_co2' were combined. The flag 'qc_sum_co2' was elliminated and 'qc_co2ppm' now 
performs range checking on 'co2ppm' variable as well as checking values of all dependencies' 
qc flags.

• flag indicating which channel isotope sample was taken from(iso)
• standard deviation of co2mv(co2mv_se)
• calculated concentration of CO2(co2ppm)
• Temperature in refigerator(t_refrig)
• base time(base_time)
• First level of QC, see warn_flag_explanation global attribute(warn_flag)
• pressure inside the IRGA box measured by the pressure controller(pres_ctrlr)
• Slope of CO2 readings during last 30sec of 3min period of raw data(co2mv_slope)
• longitude of instrument tower(site_longitude)
• latitude of instrument tower(site_latitude)
• 90% confidence limint of co2mv_slope(co2mv_slope_se)
• reading of CO2 in mV(co2mv)
• MFRSR channels(channel)
• calibration coefficient 3 (quadratic fit) 90% confidence limit(coeff3_se)
• flow rate measured by the mass flow controller(flow_rate)
• 90% confidence limit of co2ppm(co2ppm_se)
• calibration coefficient 1 (quadratic fit) 90% confidence limit(coeff1_se)
• calibration coefficient 2 (quadratic fit) 90% confidence limit(coeff2_se)
• r-squared of quadratic fit(r2)
• calibration coefficient 3 (quadratic fit)(coeff3)
• Second level of QC, see reject_flag_explanation global attribute(reject_flag)
• calibration coefficient 2 (quadratic fit)(coeff2)
• calibration coefficient 1 (quadratic fit)(coeff1)
• adjusted CO2(adj)
• height of base of instrument tower(site_elevation)
• temperature of the IRGA(t_irga)
• p-value of co2 readings during the last 30sec of 3min period of raw data(co2mv_slope_pval)
• Pressure of channel 2(pres2)
• Pressure of channel 1(pres1)
• Pressure of channel 4(pres4)
• Pressure of channel 3(pres3)
• Date and time in alternate form(yyyymmddhhmmss)
• Number of measurements for indicated channel(nmeas)
• reference CO2 reading in mV(ref)

SGP/CO2FLX/C1 - Reprocessing User Notes

Format Changes:
  To comply with archive standards, the name of the unlimited dimention variable in the 
cdf level b1 files was changed from 'record' to 'time'. This does not affect data quality.

• additive WPL H correction to c flux(fc_wpl_h)
• fractional day of the year(doy)
• mean horizontal wind speed(mean_rot_u)
• additive WPL LE correction to c flux(fc_wpl_le)
• variance of t(var_t)
• Friction velocity(ustar)
• base time(base_time)
• variance of q(var_q)
• variance of c(var_c)
• h(h)
• rotation to zero w(theta)
• height of base of instrument tower(site_elevation)
• Virtual temperature (T)(mean_t)
• Water vapor density (q)(mean_q)
• mean IRGA pressure(mean_p)
• variance of w(var_rot_w)
• variance of v(var_rot_v)
• variance of u(var_rot_u)
• Latent heat flux(le)
• Date and time in alternate form(yyyydddhhmmss)
• Vertical angle of wind(phi)
• mean co2 concentration (c)(mean_c)
• longitude of instrument tower(site_longitude)
• WPL corrected CO2 flux(fc_corr)
• Monin-Obukhov length scale(Lmoni)
• Unit Vector Wind Direction(wdir)
• Time offset of tweaks from base_time(time_offset)
• latitude of instrument tower(site_latitude)
• height of instument from tower base(zm)

• mean air temperature, lower level(t_air_lower)
• mean co2 concentration (c)(mean_c)
• depth of upper m soil probesm(z_m_soil_upper)
• base time(base_time)
• average of two upper soil temperature sensors(mean_t_soil_upper)
• Unit Vector Wind Direction(wdir)
• Vertical angle of wind(phi)
• standard error of mean_m_soil_lower(stderr_mean_m_soil_lower)
• mean relative humidity, upper level(rh_upper)
• mean air temperature, upper level(t_air_upper)
• height of upper RH/T sensor(z_upper)
• downwelling longwave hemispheric irradiance t_rad corrected(r_down_long_hemisp)
• average of four lower soil moisture sensors(mean_m_soil_lower)
• total downwelling shortwave radiation (LI-200 sensor)(r_tot)
• standard error of mean_g_soil(stderr_mean_g_soil)
• fractional day of the year(doy)
• mean IRGA pressure(mean_p)
• Water vapor density (q)(mean_q)
• Virtual temperature (T)(mean_t)
• standard error of mean_t_soil_lower note maximum of two values used in
  calculation(stderr_mean_t_soil_lower)
• average of four upper soil moisture sensors(mean_m_soil_upper)
• radiometer body temperature (for longwave correction)(t_rad)
• height of base of instrument tower(site_elevation)
• standard error of mean_t_soil_middle note maximum of two values used in
  calculation(stderr_mean_t_soil_middle)
• average of two lower soil temperature sensors(mean_t_soil_lower)
• Date and time in alternate form(yyyydddhhmmss)
• net solar radiation (NR-lite)(r_net)
• mean relative humidity, lower level(rh_lower)
• variance of w(var_rot_w)
• height of lower RH/T sensor(z_lower)
• variance of v(var_rot_v)
• height of radiation instruments(zrad)
• depth of lower t soil probesm(z_t_soil_lower)
• variance of u(var_rot_u)
• upwelling shortwave hemispheric irradiance t_rad corrected(r_up_short_hemisp)
• average of up to four soil heat flux sensors(mean_g_soil)
• rotation to zero w(theta)
• additive WPL LE correction to c flux(fc_wpl_le)
• longitude of instrument tower(site_longitude)
• Friction velocity(ustar)
• mean horizontal wind speed(mean_rot_u)
• average of two middle soil temperature sensors(mean_t_soil_middle)
• height of instument from tower base(zm)
• barometric pressure(bar_pres)
• downwelling shortwave hemispheric irradiance t_rad corrected(r_down_short_hemisp)
• additive WPL H correction to c flux(fc_wpl_h)
• Latent heat flux(le)
• depth of lower m soil probesp(z_m_soil_lower)
• depth of middle t soil probesm(z_t_soil_middle)
• Monin-Obukhov length scale(Lmoni)
• latitude of instrument tower(site_latitude)
• upwelling longwave hemispheric irradiance t_rad corrected(r_up_long_hemisp)
• depth of upper t soil probesm(z_t_soil_upper)
• Time offset of tweaks from base_time(time_offset)
• photosynthetic photon flux density (PAR)(ppfd)
• standard error of mean_m_soil_upper(stderr_mean_m_soil_upper)
• variance of t(var_t)
• standard error of mean_t_soil_upper note maximum of two values used in
  calculation(stderr_mean_t_soil_upper)
• Hourly precipitation(precip)
• variance of q(var_q)
• WPL corrected CO2 flux(fc_corr)
• variance of c(var_c)
• h(h)
• depth of soil heat flux probes(z_g_soil)

• mean co2 concentration (c)(mean_c)
• Virtual temperature (T)(mean_t)
• Friction velocity(ustar)
• mean IRGA pressure(mean_p)
• Water vapor density (q)(mean_q)
• Unit Vector Wind Direction(wdir)
• height of instument from tower base(zm)
• Time offset of tweaks from base_time(time_offset)
• latitude of instrument tower(site_latitude)
• Date and time in alternate form(yyyydddhhmmss)
• variance of v(var_rot_v)
• variance of u(var_rot_u)
• variance of w(var_rot_w)
• WPL corrected CO2 flux(fc_corr)
• h(h)
• variance of t(var_t)
• rotation to zero w(theta)
• fractional day of the year(doy)
• base time(base_time)
• Vertical angle of wind(phi)
• longitude of instrument tower(site_longitude)
• variance of q(var_q)
• variance of c(var_c)
• mean horizontal wind speed(mean_rot_u)
• additive WPL H correction to c flux(fc_wpl_h)
• Monin-Obukhov length scale(Lmoni)
• Latent heat flux(le)
• height of base of instrument tower(site_elevation)
• additive WPL LE correction to c flux(fc_wpl_le)

• variance of c(var_c)
• height of instument from tower base(zm)
• Date and time in alternate form(yyyydddhhmmss)
• Water vapor density (q)(mean_q)
• mean IRGA pressure(mean_p)
• additive WPL H correction to c flux(fc_wpl_h)
• Virtual temperature (T)(mean_t)
• Time offset of tweaks from base_time(time_offset)
• base time(base_time)
• height of base of instrument tower(site_elevation)
• mean co2 concentration (c)(mean_c)
• Vertical angle of wind(phi)
• variance of t(var_t)
• variance of q(var_q)
• Monin-Obukhov length scale(Lmoni)
• Unit Vector Wind Direction(wdir)
• longitude of instrument tower(site_longitude)
• latitude of instrument tower(site_latitude)
• variance of u(var_rot_u)
• variance of v(var_rot_v)
• variance of w(var_rot_w)
• mean horizontal wind speed(mean_rot_u)
• fractional day of the year(doy)
• h(h)
• Friction velocity(ustar)
• Latent heat flux(le)
• WPL corrected CO2 flux(fc_corr)
• rotation to zero w(theta)
• additive WPL LE correction to c flux(fc_wpl_le)

SGP/CO2FLX/C1 - Reprocessing User Notes

A subset of the radiation measurements had an incorrect gain applied to raw data in period 
from 20021218-20031218.  To correct for this, a multiplicative correction factor of 1.11 
were applied to raw data used for the following variables:

r_down_short_hemisp
r_down_long_hemisp
r_up_short_hemisp
r_up_long_hemisp

Note that the long wave variables are computed by adding the black body thermal radiation 
from the radiometer body to each of the long wave signals.  Hence, the multiplicative 
correction is applied to the raw long wave fluxes before adding in the flux from the 
radiometer body.

• downwelling shortwave hemispheric irradiance t_rad corrected(r_down_short_hemisp)
• upwelling longwave hemispheric irradiance t_rad corrected(r_up_long_hemisp)
• upwelling shortwave hemispheric irradiance t_rad corrected(r_up_short_hemisp)
• downwelling longwave hemispheric irradiance t_rad corrected(r_down_long_hemisp)

SGP/CO2FLX/C1 - Longwave Radiation Incorrect

Long wave radiation values (r_up_long_hemisp, r_down_long_hemisp) are bad 
due to correction with bad radiometer body temperature (t_rad) resulting
from a wiring issue.

• radiometer body temperature (for longwave correction)(t_rad)
• upwelling longwave hemispheric irradiance t_rad corrected(r_up_long_hemisp)
• downwelling longwave hemispheric irradiance t_rad corrected(r_down_long_hemisp)

SGP/PGS/C1 - Reprocessing User Notes

Precise Gas System (pgs) daily b1 files should have a dimension of 480, corresponding to a 
measurement every 3 minutes. Previously submitted files had a dimension of 481, the last 
time step of each individual file being mistakenly repeated.

• flag indicating which channel isotope sample was taken from(iso)
• standard deviation of co2mv(co2mv_se)
• calculated concentration of CO2(co2ppm)
• Temperature in refigerator(t_refrig)
• base time(base_time)
• First level of QC, see warn_flag_explanation global attribute(warn_flag)
• pressure inside the IRGA box measured by the pressure controller(pres_ctrlr)
• Slope of CO2 readings during last 30sec of 3min period of raw data(co2mv_slope)
• longitude of instrument tower(site_longitude)
• latitude of instrument tower(site_latitude)
• 90% confidence limint of co2mv_slope(co2mv_slope_se)
• reading of CO2 in mV(co2mv)
• MFRSR channels(channel)
• calibration coefficient 3 (quadratic fit) 90% confidence limit(coeff3_se)
• flow rate measured by the mass flow controller(flow_rate)
• 90% confidence limit of co2ppm(co2ppm_se)
• calibration coefficient 1 (quadratic fit) 90% confidence limit(coeff1_se)
• calibration coefficient 2 (quadratic fit) 90% confidence limit(coeff2_se)
• r-squared of quadratic fit(r2)
• calibration coefficient 3 (quadratic fit)(coeff3)
• Second level of QC, see reject_flag_explanation global attribute(reject_flag)
• calibration coefficient 2 (quadratic fit)(coeff2)
• calibration coefficient 1 (quadratic fit)(coeff1)
• adjusted CO2(adj)
• height of base of instrument tower(site_elevation)
• temperature of the IRGA(t_irga)
• p-value of co2 readings during the last 30sec of 3min period of raw data(co2mv_slope_pval)
• Pressure of channel 2(pres2)
• Pressure of channel 1(pres1)
• Pressure of channel 4(pres4)
• Pressure of channel 3(pres3)
• Date and time in alternate form(yyyymmddhhmmss)
• Number of measurements for indicated channel(nmeas)
• reference CO2 reading in mV(ref)

SGP/CO2FLX/C1 - Reprocess: Units

Mean CO2 density units are incorrectly labeled as umol m-3. Units should be labeled as 
mmol m-3.

• mean co2 concentration (c)(mean_c)

• mean co2 concentration (c)(mean_c)

• mean co2 concentration (c)(mean_c)

SGP/CO2FLX/C1 - Mean CO2 density incorrect, CO2 flux suspect

A problem was identified with the calibration of the instrument over the time period 
October 12, 2004 to October 20, 2004. The offset of the instrument is known to be incorrect 
over this time frame, and a study of the gain of the instrument is underway.

• mean co2 concentration (c)(mean_c)
• WPL corrected CO2 flux(fc_corr)

SGP/PGS/C1 - Incorrect 60m Data

Precise Gas system (PGS) data at 60m (channel 4) are incorrect. This problem is due to a 
freezing rain and ice storm that hit SGP Central facility on January 5, 2005. The 60m 
tower inlet was clogged with ice and consequently, no air was supplied to the PGS instrument.

• pressure inside the IRGA box measured by the pressure controller(pres_ctrlr)
• flow rate measured by the mass flow controller(flow_rate)
• Slope of CO2 readings during last 30sec of 3min period of raw data(co2mv_slope)
• standard deviation of co2mv(co2mv_se)
• 90% confidence limit of co2ppm(co2ppm_se)
• calculated concentration of CO2(co2ppm)
• 90% confidence limint of co2mv_slope(co2mv_slope_se)
• p-value of co2 readings during the last 30sec of 3min period of raw data(co2mv_slope_pval)
• Pressure of channel 4(pres4)
• reading of CO2 in mV(co2mv)

SGP/CO2FLX/C1 - Reprocessed: User Notes

Replacement of LI-200 sensor (total downwelling shortwave radiation, variable r_tot) by a 
new LI-190 sensor (upwelling photosynthetic photon flux density, variable ppfd_up).

The new LI-190 sensor was:
- installed on December 9, 2004. 
- being tested from December 9, 2004 to December 22, 2004.
- operational after December 22, 2004.

Consequently:
1. variable "r_tot" is filled with missing values (qc_r_tot = 1) after December 9, 2004,
2. variable "ppfd_up" is filled with missing values (qc_ppfd_up = 1) prior December 22, 
2004.

• photosynthetic photon flux density (PAR)(ppfd_up)
• total downwelling shortwave radiation (LI-200 sensor)(r_tot)

SGP/CO2FLX/C1 - downwelling longwave hemispheric irradiance incorrect

A problem was identified with the downwelling longwave hemispheric irradiance (variable 
"r_down_long_hemisp") calibration of our Kipp & Zonen CNR1 radiometer. The offset of the 
instrument is believed to be incorrect over the specified time frame, and a correction of 
the problem is underway.

• downwelling longwave hemispheric irradiance t_rad corrected(r_down_long_hemisp)

SGP/CO2FLX/C1 - Soil Temperature measurements

Current data quality check (qc) procedure does not catch spikes in soil temperature 
measurements. A new qc procedure is being tested and will improve the current procedure.

• average of two upper soil temperature sensors(mean_t_soil_upper)
• average of two middle soil temperature sensors(mean_t_soil_middle)
• average of two lower soil temperature sensors(mean_t_soil_lower)

SGP/PGS/C1 - Suspicious 4m data

KNF pump for 4m height (channel 2) started to leak on November 24, 2004 and sampled air 
was consequently "contaminated" by indoor air. The pump was replaced on August 19, 2005.

• 90% confidence limit of co2ppm(co2ppm_se)
• calculated concentration of CO2(co2ppm)

SGP/PGS/C1 - Suspicious 2m data

KNF pump for 2m height (channel 1) started to leak on July 22, 2004 and sampled air was 
consequently "contaminated" by indoor air. The pump was replaced on August 19, 2005.

• 90% confidence limit of co2ppm(co2ppm_se)
• calculated concentration of CO2(co2ppm)

SGP/PGS/C1 - Suspicious 25m and 60m data

KNF pumps for 25m and 60m height (channel 3 and channel 4) started to leak on March 31, 
2005 and sampled air was consequently "contaminated" by indoor air. The pumps were replaced 
on August 19, 2005.

• 90% confidence limit of co2ppm(co2ppm_se)
• calculated concentration of CO2(co2ppm)

SGP/PGS/C1 - Updated files

Dew point temperature (dpt) sensor (Vaisala DMT 142) was added to the system on May 24, 
2005 to assess water trapping system efficiency. Consequently, variable "dpt" is filled 
with missing values (-999.99) prior measurements start date (May 24, 2005).

• flag indicating which channel isotope sample was taken from(iso)
• standard deviation of co2mv(co2mv_se)
• calculated concentration of CO2(co2ppm)
• Temperature in refigerator(t_refrig)
• base time(base_time)
• First level of QC, see warn_flag_explanation global attribute(warn_flag)
• pressure inside the IRGA box measured by the pressure controller(pres_ctrlr)
• Slope of CO2 readings during last 30sec of 3min period of raw data(co2mv_slope)
• longitude of instrument tower(site_longitude)
• latitude of instrument tower(site_latitude)
• 90% confidence limint of co2mv_slope(co2mv_slope_se)
• reading of CO2 in mV(co2mv)
• MFRSR channels(channel)
• calibration coefficient 3 (quadratic fit) 90% confidence limit(coeff3_se)
• flow rate measured by the mass flow controller(flow_rate)
• 90% confidence limit of co2ppm(co2ppm_se)
• calibration coefficient 1 (quadratic fit) 90% confidence limit(coeff1_se)
• calibration coefficient 2 (quadratic fit) 90% confidence limit(coeff2_se)
• r-squared of quadratic fit(r2)
• calibration coefficient 3 (quadratic fit)(coeff3)
• Second level of QC, see reject_flag_explanation global attribute(reject_flag)
• calibration coefficient 2 (quadratic fit)(coeff2)
• calibration coefficient 1 (quadratic fit)(coeff1)
• adjusted CO2(adj)
• height of base of instrument tower(site_elevation)
• temperature of the IRGA(t_irga)
• p-value of co2 readings during the last 30sec of 3min period of raw data(co2mv_slope_pval)
• Pressure of channel 2(pres2)
• Pressure of channel 1(pres1)
• Pressure of channel 4(pres4)
• Pressure of channel 3(pres3)
• Date and time in alternate form(yyyymmddhhmmss)
• Number of measurements for indicated channel(nmeas)
• reference CO2 reading in mV(ref)

SGP/CO2FLX/C1 - Reprocess: calibration error

A problem was identified with the calibration of the instrument performed on May 27, 2005. 
A study to correct this bad calibration is underway.

• Water vapor density (q)(mean_q)
• WPL corrected CO2 flux(fc_corr)
• Latent heat flux(le)

SGP/CO2FLX/C1 - Met stand was moved

Ameriflux program (Hank Loescher from Oregon state university) visits the site to 
intercompare his instruments with our 4m flux system.
The met stand was moved by 30 feet and consequently:
1. Soil moisture sensors were disconnected,
2. Soil temperature sensors were disconnected,
3. Soil heat plates were disconnected,
4. The true direction of the anemometer boom was 230 degrees instead of the regular 270 
degrees.

• average of four upper soil moisture sensors(mean_m_soil_upper)
• average of four lower soil moisture sensors(mean_m_soil_lower)
• average of two upper soil temperature sensors(mean_t_soil_upper)
• Unit Vector Wind Direction(wdir)
• average of two middle soil temperature sensors(mean_t_soil_middle)
• average of two lower soil temperature sensors(mean_t_soil_lower)
• average of up to four soil heat flux sensors(mean_g_soil)

SGP/CO2FLX/C1 - downwelling longwave hemispheric irradiance incorrect

Downwelling longwave radiation measurements (variable "r_down_long_hemisp") are bad due to 
a wiring issue. Users should not use the downwelling longwave hemispheric irradiance 
during this period. The downwelling shortwave and longwave radiation at CF is also available 
from the Broadband Radiometer Station (BRS).

• downwelling longwave hemispheric irradiance t_rad corrected(r_down_long_hemisp)

SGP/CO2FLX/C1 - Disturbance around site

A bulldozer used to excavate the SGP Tower anchors was right around (within 10 feet) our 
systems.

• WPL corrected CO2 flux(fc_corr)
• mean co2 concentration (c)(mean_c)

• WPL corrected CO2 flux(fc_corr)
• mean co2 concentration (c)(mean_c)

• mean co2 concentration (c)(mean_c)
• WPL corrected CO2 flux(fc_corr)

• WPL corrected CO2 flux(fc_corr)
• mean co2 concentration (c)(mean_c)

SGP/CO2FLX/C1 - Farm operation

Soil temperature, soil moisture, soil heat flux and upwelling surface radiation (long, 
short, and PAR) measurements were not valid from 20070822 to 20070907 due to farm operations.

• standard error of mean_t_soil_lower note maximum of two values used in
  calculation(stderr_mean_t_soil_lower)
• average of four upper soil moisture sensors(mean_m_soil_upper)
• standard error of mean_m_soil_lower(stderr_mean_m_soil_lower)
• upwelling shortwave hemispheric irradiance t_rad corrected(r_up_short_hemisp)
• standard error of mean_m_soil_upper(stderr_mean_m_soil_upper)
• standard error of mean_t_soil_middle note maximum of two values used in
  calculation(stderr_mean_t_soil_middle)
• average of two lower soil temperature sensors(mean_t_soil_lower)
• average of up to four soil heat flux sensors(mean_g_soil)
• standard error of mean_t_soil_upper note maximum of two values used in
  calculation(stderr_mean_t_soil_upper)
• photosynthetic photon flux density (PAR)(ppfd_up)
• average of four lower soil moisture sensors(mean_m_soil_lower)
• upwelling longwave hemispheric irradiance t_rad corrected(r_up_long_hemisp)
• average of two upper soil temperature sensors(mean_t_soil_upper)
• standard error of mean_g_soil(stderr_mean_g_soil)
• average of two middle soil temperature sensors(mean_t_soil_middle)

SGP/CO2FLX/C1 - Reprocess: 4m instruments height

The height of the 4m instruments is 4.8 m and not 4.65 m as shown in b1 datastream

• height of instument from tower base(zm)

SGP/CO2FLX/C1 - Reprocessed: Recalibration

The 4m CO2 flux system was calibrated on May 25, 2005. After the calibration was 
performed, calibration coefficients used to measure CO2 density were not updated. This added an 
OFFSET to the CO2 density measurements.

The data have been reprocessed to address the offset.  The reprocessed data were archived 
in December 2008. Please retrieve the updated files for use in your analysis.

• mean co2 concentration (c)(mean_c)