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  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">BG</journal-id>
<journal-title-group>
<journal-title>Biogeosciences</journal-title>
<abbrev-journal-title abbrev-type="publisher">BG</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Biogeosciences</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1726-4189</issn>
<publisher><publisher-name>Copernicus GmbH</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/bg-12-415-2015</article-id><title-group><article-title>Intercomparison of fast response commercial gas analysers for nitrous
oxide flux measurements under field conditions</article-title>
      </title-group><?xmltex \runningtitle{Intercomparison of fast response commercial gas analysers}?><?xmltex \runningauthor{\"{U}.~Rannik et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Rannik</surname><given-names>Ü.</given-names></name>
          <email>ullar.rannik@heuristica.ee</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Haapanala</surname><given-names>S.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Shurpali</surname><given-names>N. J.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-1052-4396</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Mammarella</surname><given-names>I.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-8516-3356</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Lind</surname><given-names>S.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-7701-533X</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Hyvönen</surname><given-names>N.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Peltola</surname><given-names>O.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-1744-6290</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Zahniser</surname><given-names>M.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Martikainen</surname><given-names>P. J.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Vesala</surname><given-names>T.</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>Department of Physics, P.O. Box 48, 00014 University of Helsinki,
Helsinki, Finland</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Department of Environmental Science, University of Eastern Finland,
Kuopio, Finland</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Center for Atmospheric and Environmental Chemistry, Aerodyne Research
Inc., Billerica, MA, USA</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Ü. Rannik (ullar.rannik@heuristica.ee)</corresp></author-notes><pub-date><day>22</day><month>January</month><year>2015</year></pub-date>
      
      <volume>12</volume>
      <issue>2</issue>
      <fpage>415</fpage><lpage>432</lpage>
      <history>
        <date date-type="received"><day>19</day><month>May</month><year>2014</year></date>
           <date date-type="rev-request"><day>1</day><month>August</month><year>2014</year></date>
           <date date-type="rev-recd"><day>28</day><month>November</month><year>2014</year></date>
           <date date-type="accepted"><day>11</day><month>December</month><year>2014</year></date>
           
      </history>
      <permissions>
<license license-type="open-access">
<license-p>This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link></license-p>
</license>
</permissions><self-uri xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015.html">This article is available from https://www.biogeosciences.net/12/415/2015/bg-12-415-2015.html</self-uri>
<self-uri xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015.pdf">The full text article is available as a PDF file from https://www.biogeosciences.net/12/415/2015/bg-12-415-2015.pdf</self-uri>


      <abstract>
    <p>Four gas analysers capable of measuring nitrous oxide (N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O)
concentration at a response time necessary for eddy covariance flux
measurements were operated from spring until winter 2011 over a field
cultivated with reed canary grass (RCG, <italic>Phalaris arundinacea</italic>, L.),
a perennial bioenergy crop in eastern Finland. The instruments were TGA100A
(Campbell Scientific Inc.), CW-TILDAS-CS (Aerodyne Research Inc.),
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d (Los Gatos Research Inc.) and QC-TILDAS-76-CS (Aerodyne
Research Inc.). The period with high emissions, lasting for about 2 weeks
after fertilization in late May, was characterized by an up to 2 orders of
magnitude higher emission, whereas during the rest of the campaign the
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes were small, from 0.01 to 1 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Two
instruments, CW-TILDAS-CS and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d, determined the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
exchange with minor systematic difference throughout the campaign, when
operated simultaneously. TGA100A produced the cumulatively highest N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
estimates (with 29 % higher values during the period when all instruments
were operational). QC-TILDAS-76-CS obtained 36 % lower fluxes than
CW-TILDAS-CS during the first period, including the emission episode, whereas
the correspondence with other instruments during the rest of the campaign was
good. The reasons for systematic differences were not identified, suggesting
further need for detailed evaluation of instrument performance under field
conditions with emphasis on stability, calibration and any other factors that
can systematically affect the accuracy of flux measurements. The instrument
CW-TILDAS-CS was characterized by the lowest noise level (with a standard
deviation of around 0.12 ppb at 10 Hz sampling rate) as compared to
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d and QC-TILDAS-76-CS (around 0.50 ppb) and TGA100A
(around 2 ppb). We identified that for all instruments except CW-TILDAS-CS
the random error due to instrumental noise was an important source of
uncertainty at the 30 min averaging level and the total stochastic error was
frequently of the same magnitude as the fluxes when N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O exchange was
small at the measurement site. Both instruments based on continuous-wave quantum cascade laser, CW-TILDAS-CS and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d, were able to
determine the same sample of low N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes with a high mutual coefficient
of determination at the 30 min averaging level and with minor systematic
difference over the observation period of several months. This enables us to
conclude that the new-generation instrumentation is capable of measuring
small N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O exchange with high precision and accuracy at sites with low
fluxes.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p>Instrumental characteristics. Experimental precision values are
based on flux measurements during the period DOY 206–271 (period II). TDL –
tunable diode laser; CW-QCL – continuous-wave quantum cascade laser; P-QCL –
pulsed QCL. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mn>10</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>P</mml:mi><mml:mn>50</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>P</mml:mi><mml:mn>90</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> represent the lower percentile, median and upper percentile values.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Instrument</oasis:entry>  
         <oasis:entry colname="col2">TGA100A</oasis:entry>  
         <oasis:entry colname="col3">CW-TILDAS-CS</oasis:entry>  
         <oasis:entry colname="col4">N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d</oasis:entry>  
         <oasis:entry colname="col5">QC-TILDAS-76-CS</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">model</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Manufacturer</oasis:entry>  
         <oasis:entry colname="col2">Campbell</oasis:entry>  
         <oasis:entry colname="col3">Aerodyne</oasis:entry>  
         <oasis:entry colname="col4">Los Gatos</oasis:entry>  
         <oasis:entry colname="col5">Aerodyne</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Scientific Inc.</oasis:entry>  
         <oasis:entry colname="col3">Research Inc.</oasis:entry>  
         <oasis:entry colname="col4">Research Inc.</oasis:entry>  
         <oasis:entry colname="col5">Research Inc.</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Abbrev. used in</oasis:entry>  
         <oasis:entry colname="col2">CS-TDL</oasis:entry>  
         <oasis:entry colname="col3">AR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col4">LGR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col5">AR-P-QCL</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">current study</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Measured species</oasis:entry>  
         <oasis:entry colname="col2">N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O</oasis:entry>  
         <oasis:entry colname="col3">N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, CO</oasis:entry>  
         <oasis:entry colname="col4">N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, CO</oasis:entry>  
         <oasis:entry colname="col5">N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Sample cell</oasis:entry>  
         <oasis:entry colname="col2">480</oasis:entry>  
         <oasis:entry colname="col3">500</oasis:entry>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5">500 (76 m</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">volume (mL)</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5">path length)</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Sample cell</oasis:entry>  
         <oasis:entry colname="col2">50</oasis:entry>  
         <oasis:entry colname="col3">53</oasis:entry>  
         <oasis:entry colname="col4">117</oasis:entry>  
         <oasis:entry colname="col5">53</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">pressure (hPa)</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Spectroscopic</oasis:entry>  
         <oasis:entry colname="col2">0.00 (drier used</oasis:entry>  
         <oasis:entry colname="col3">0.39</oasis:entry>  
         <oasis:entry colname="col4">0.00 (built-in</oasis:entry>  
         <oasis:entry colname="col5">0.0235</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">correction</oasis:entry>  
         <oasis:entry colname="col2">in sampling</oasis:entry>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4">correction by</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">coefficient <inline-formula><mml:math display="inline"><mml:mi>b</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2">line)</oasis:entry>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4">the instrument)</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Precision, 10 Hz</oasis:entry>  
         <oasis:entry colname="col2">1.89/1.98/2.1</oasis:entry>  
         <oasis:entry colname="col3">0.12/0.12/0.14</oasis:entry>  
         <oasis:entry colname="col4">0.46/0.60/0.78</oasis:entry>  
         <oasis:entry colname="col5">0.43/0.46/0.51</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">noise SD,</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mn>10</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mn>50</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mn>90</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">this study (ppb)</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p>During the last few years there has been a rapid development in the application
of laser spectroscopy for greenhouse gas measurements. In particular, the
development of fast response N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O analysers based on spectroscopic
techniques (e.g. tunable diode laser (TDL) and quantum cascade laser (QCL)
spectrometers) has facilitated the eddy covariance (EC) measurements of
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O exchange in different ecosystems. Such measurements have been
reported in literature and they have been carried out in different ecosystems
such as agricultural (Smith et al., 1994; Wienhold et al., 1994; Christensen
et al., 1996; Laville et al., 1997; Scanlon and Kiely, 2003; Neftel et al.,
2007; Kroon et al., 2007) and forest (Pihlatie et al., 2005; Eugster et al.,
2007), and over urban canopies (Famulari et al., 2010; Järvi et al.,
2014).</p>
      <p>The observed N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O emissions are episodic in nature, showing high spatial
and temporal variability. Emission bursts of short duration, typically
occurring after fertilizer application, or associated with thawing and rain
events (Kroon et al., 2007; Pihlatie et al., 2010), are followed by long
periods of small fluxes, when uptake of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O has also been observed
(Flechard et al., 2005). Overall, N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes reported by previous
studies are characterized by large uncertainties and temporal variability,
which are related to biogeochemical soil processes and several systematic and
random error sources of the EC measurements. One of the sources of
uncertainty for the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes measured by the EC technique is the
performance and stability of fast response gas analysers. Some studies
performed under field conditions (Eugster et al., 2007; Kroon et al., 2007;
Neftel et al., 2009) have reported that laser drift can cause occasional
over- or under-estimation of EC flux. Instrumental drift is typically
characteristic of TDL as well as QCL spectrometers (Werle et al., 1993; Nelson et
al., 2002). Mammarella et al. (2010) thoroughly investigated the performance
of TDL instruments in measurements of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes by the EC technique.
They suggested that high-pass filtering could be used to remove the
low-frequency signal drifting, which could otherwise contaminate the detected
concentration time series and significantly increase the flux uncertainty.</p>
      <p>Apart from episodic emissions, N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes are typically small in
magnitude (of the order of 1 to 100 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g N m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>,
which corresponds to N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O flux range from 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> to
1 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> as presented in the units used in the current
study), being on the detection limit of the EC systems (e.g. Pihlatie et al.,
2005; Wang et al., 2013). Small fluxes imply small turbulent fluctuations of concentration, requiring high instrument precision to
resolve those fluctuations. In other words, the ratio of signal (turbulent
fluctuations) to instrumental noise has to be high enough to achieve
sufficiently low flux error arising from the noise present in measured
signals (Lenschow and Kristensen, 1985).</p>
      <p>The goals of this study are to compare the available equipment for N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
flux measurements employing the EC technique and to evaluate their
performance, ability to detect small fluxes and long-term stability in
determining the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O exchange. The instruments used were TGA100A
(Campbell Scientific Inc.), CW-TILDAS-CS (Aerodyne Research Inc.),
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d (Los Gatos Research Inc.) and QC-TILDAS-76-CS (Aerodyne
Research Inc.), which shall be further referred to as CS-TDL, AR-CW-QCL,
LGR-CW-QCL and AR-P-QCL, respectively, throughout this study by using the
combinations of acronyms for manufacturer and the laser type (see Table 1).
In addition, the methods for flux calculation using the laser spectrometer
data are evaluated and the magnitude and dynamics of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes during
the reed canary grass (RCG) growing season are determined.</p>
</sec>
<sec id="Ch1.S2">
  <title>Materials and methods</title>
<sec id="Ch1.S2.SS1">
  <title>Site</title>
      <p>The measurement site was a 6.9 ha field cultivated with RCG, a perennial
bioenergy crop. The site was located in the rural area of Maaninka  (merged with the city of Kuopio 1 January 2015), eastern
Finland (63<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>9<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula>48.69<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>′</mml:mo><mml:mo>′</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula> N, 27<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>14<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula>3.29<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>′</mml:mo><mml:mo>′</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula> E). Long-term
(reference period 1981–2010; Pirinen et al., 2012) annual air temperature
in the region is 3.2 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, the coldest month of the year is February
and the warmest is July, with monthly mean air temperature being <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>9.4 and
17.0 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, respectively. The annual precipitation in the region is 612
mm. Part of this precipitation amount falls as snow. Snow cover season starts
in October and lasts until the end of April with a maximum snow cover of
approximately 50 cm. The RCG crop at the Maaninka site was fertilized in the
beginning of the growing season (late May), resulting in a large emission
pulse of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O. The site was applied with an N–P–K–S fertilizer containing
76 kg N ha<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, based on ammonium nitrate
(NO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>–N <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> NH<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>–N <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mn>47</mml:mn><mml:mo>:</mml:mo><mml:mn>53</mml:mn></mml:mrow></mml:math></inline-formula>). The canopy height developed
throughout the growing season from about 10 cm in mid-May to 1.7 m by late
June. The increase in plant height was almost linear in the period between these
two times, and from July onwards plant height grew slowly up to 1.9 m.</p>
      <p>The soil at the study site is classified as fine sand to coarse silt
(particle size 0.03–0.06 mm). According to the World Reference Base for
Soil Resources (WRB) system (FAO, 2006), the soil is classified as Regosol.
The soil pH varies from 5.4 to 6.1 within the ploughing depth from the
surface to about 30 cm, electrical conductivity between
960 and 3060<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>s cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and soil organic matter content between 3 and
11 %. The average C <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> N ratio in the ploughing depth is 14.9 (ranging
from 14.1 to 15.7). The soil particle density is about 2.65 g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
within the soil depth from the surface to about 20 cm.</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Measurements</title>
      <p>Measurements were conducted by the University of Helsinki (UH) and by the
University of Eastern Finland (UEF), operating separate EC systems based on
two different sonic anemometers. The UH measurement set-up included a 3-D
ultrasonic anemometer (USA-1, METEK GmbH, Elmshorn, Germany) to acquire the
wind components. The anemometer was installed on top of a pole, with a
measurement height of 2.2 m. The measurement height was raised to 2.4 m
on 30 June 2011 due to the RCG growth. The gas analysers were situated in an air
conditioned cabin located about 15 m east from the anemometer pole. This
wind direction (50–110<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> sector) was therefore discarded from further
analysis due to possible disturbances to flux measurements. Sample inlets for
gas analysers were located 10 cm below the anemometer. The N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
instruments operated by the UH were the instrument based on tunable diode
laser CS-TDL (model TGA100A, Campbell Scientific Inc.) and two instruments
based on continuous-wave quantum cascade lasers, AR-CW-QCL (models
CW-TILDAS-CS, Aerodyne Research Inc., see e.g. Zahniser et al., 2009; Lee et
al., 2011) and LGR-CW-QCL (model N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> CO-23d, Los Gatos Research
Inc., see e.g. Provencal et al., 2005). Sampling lines of AR-CW-QCL and
LGR-CW-QCL were heated slightly above ambient temperature in order to
prevent water condensing on the lines. CS-TDL used a dryer just before the
instrument and no sampling line heating was used. The flow rates and tube
dimensions were chosen to correspond to a turbulent flow regime except that the
larger diameter of the sampling line of the LGR-CW-QCL analyser resulted in a
laminar tube flow for that instrument (see Sect. 3.1 below). Further details
of the instruments used are given in Table 1 and details of the different
set-ups are given in Table 2.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><caption><p>Eddy covariance measurement set-up, flux calculation and quality
screening parameters.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="justify" colwidth="79.667717pt"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Instrument</oasis:entry>  
         <oasis:entry colname="col2">CS-TDL</oasis:entry>  
         <oasis:entry colname="col3">AR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col4">LGR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col5">AR-P-QCL</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Sampling height (m)</oasis:entry>  
         <oasis:entry colname="col2">2.2/2.4</oasis:entry>  
         <oasis:entry colname="col3">2.2/2.4</oasis:entry>  
         <oasis:entry colname="col4">2.4</oasis:entry>  
         <oasis:entry colname="col5">2.0/2.5</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Horizontal separation<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">1</mml:mn></mml:msup></mml:math></inline-formula> (m)</oasis:entry>  
         <oasis:entry colname="col2">0.05</oasis:entry>  
         <oasis:entry colname="col3">0.05</oasis:entry>  
         <oasis:entry colname="col4">0.07</oasis:entry>  
         <oasis:entry colname="col5">0.1</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Tube inner<?xmltex \hack{\hfill\break}?>diameter (mm)</oasis:entry>  
         <oasis:entry colname="col2">4</oasis:entry>  
         <oasis:entry colname="col3">4</oasis:entry>  
         <oasis:entry colname="col4">8</oasis:entry>  
         <oasis:entry colname="col5">4</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Tube length (m)</oasis:entry>  
         <oasis:entry colname="col2">17.8</oasis:entry>  
         <oasis:entry colname="col3">16</oasis:entry>  
         <oasis:entry colname="col4">16</oasis:entry>  
         <oasis:entry colname="col5">8.5</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Flow rate (LPM)</oasis:entry>  
         <oasis:entry colname="col2">17</oasis:entry>  
         <oasis:entry colname="col3">13.2</oasis:entry>  
         <oasis:entry colname="col4">11.6</oasis:entry>  
         <oasis:entry colname="col5">13.5</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Lag time<?xmltex \hack{\hfill\break}?>from tube flow (s)</oasis:entry>  
         <oasis:entry colname="col2">0.79</oasis:entry>  
         <oasis:entry colname="col3">0.91</oasis:entry>  
         <oasis:entry colname="col4">4.2</oasis:entry>  
         <oasis:entry colname="col5">0.48</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Lag time window<?xmltex \hack{\hfill\break}?>used in flux<?xmltex \hack{\hfill\break}?>calculation (s)</oasis:entry>  
         <oasis:entry colname="col2">1.0 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.0</oasis:entry>  
         <oasis:entry colname="col3">1.0 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.0</oasis:entry>  
         <oasis:entry colname="col4">1.0 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.0<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">1.0 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.8<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Time constant<?xmltex \hack{\hfill\break}?>used in spectral<?xmltex \hack{\hfill\break}?>corrections (s)</oasis:entry>  
         <oasis:entry colname="col2">0.12</oasis:entry>  
         <oasis:entry colname="col3">0.07</oasis:entry>  
         <oasis:entry colname="col4">0.26</oasis:entry>  
         <oasis:entry colname="col5">0.15</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p><inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">1</mml:mn></mml:msup></mml:math></inline-formula> Refers to separation of the sampling inlet from the centre position of
the sonic anemometer. Vertical separation was 0.1 m for all instruments.
<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> Prior to flux calculation the concentration records of LGR-CW-QCL were
synchronized with AR-CW-QCL outputs.
<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> The lag time window was used to determine the lag time for CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>,
which was assigned as the lag time for N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O.</p></table-wrap-foot></table-wrap>

      <p>The maintenance of CS-TDL was the most demanding of the compared
instruments. It uses liquid nitrogen to keep the laser source at the
operating temperature, and the Dewar was filled up twice a week. The
instrument CS-TDL was calibrated in the beginning of the campaign. Further,
the operating parameters of the analyser, such as laser current and laser,
housing and detector temperatures, were checked once a week and after power
failures. In addition, the shape and intensity of the absorption line were
checked at the same time. These checks were assumed to guarantee calibration
stability of the instrument to a reasonable degree. In addition, the inlet
filter of CS-TDL was changed once a month.</p>
      <p>The AR-CW-QCL was calibrated and its operating parameters were
fine-tuned at the site after instrument installation. The instrument
manufacturer provided a software upgrade during the campaign to conduct the
real-time water vapour correction to the trace gas concentration data
analysed by the instrument. In addition, the operating parameters were
fine-tuned a few times on-line by the instrument manufacturer during the
campaign.</p>
      <p>LGR-CW-QCL was used in the campaign later (see Sect. 2.6 for details). The
factory calibration of LGR-CW-QCL was checked but no deviation was observed
within the uncertainty range of the calibration gases. After about 2 weeks
of operation, the laser drifted out of the tuning range and the laser offset
current was tuned manually to enable correct operation again. No calibration
of the instruments AR-CW-QCL and LGR-CW-QCL was performed during the campaign as
these analysers were expected to be very stable according to manufacturers'
information.</p>
      <p>The UEF set-up included a pulsed quantum cascade laser spectrometer AR-P-QCL
(model QC-TILDAS-76-CS, Aerodyne Research Inc., Billerica, MS, USA, see
McManus et al., 2005), an infrared gas analyser (IRGA, model Li-6262) and a
3-D sonic anemometer (model R3-50, Gill Instruments, Ltd., Hampshire, UK) for
fast response gas concentration and wind component measurements (Tables 1 and
2). The heated intake tubes for the laser spectrometer and IRGA were
installed on either side of the sonic anemometer, all mounted on a boom on
an adjustable instrument mast. The mast height was set at 2.0 m above the
soil surface in the beginning of the campaign. To adjust to the increasing
plant height, the mast was raised to 2.5 m during mid-June. AR-P-QCL was set
up to measure the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and water vapour mixing
ratios simultaneously, while the IRGA was used to monitor the CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and water vapour
mixing ratios. Both trace gas analysers were calibrated against standard
gases a minimum of once a month during the campaign; in particular, AR-P-QCL was
calibrated every 2–3 weeks with two standard gases of 299 and 342 ppb. The
calibration slope of AR-P-QCL did not change by more than 7.6 %
throughout the campaign and maximum 6.1 % between consecutive
calibrations. Thus, 6.1 % can be considered as the maximum flux systematic
error arising from calibration accuracy of this instrument.</p>
      <p>A weather station set up on another mast close to the EC mast monitored the
supporting meteorological variables. The weather station mast height was also
adjusted according to the changes in the EC mast height. Supporting
measurements included air temperature and relative humidity (model: HMP45C,
Vaisala Inc.) using radiation shield, atmospheric pressure (model CS106
Vaisala PTB110 Barometer), wind speed and direction (model 03002-5,
R.M. Young Company) and several other variables not used in the current study.
Data were collected using a datalogger (model CR3000, Campbell Scientific
Inc.). Except air pressure (stored as hourly averages), meteorological data
were stored as 30 min averages. Short gaps in the data were filled using
linear interpolation, but when air temperature, relative humidity, pressure
or rainfall data were missing for longer periods, data from Maaninka weather
station operated by the Finnish Meteorological Institute located about 6 km
south-east from the site were used.</p>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Flux processing</title>
      <p>Measurements were sampled at 10 Hz frequency. In order to eliminate spikes, filtering
was performed according to the standard approach (Vickers and Mahrt, 1997), where
the high-frequency EC data were de-spiked by comparing two adjacent
measurements. If the difference between two adjacent concentration
measurements of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O was greater than 20 ppb, the following point was
replaced with the same value as the previous point.</p>
      <p>The spectroscopic correction due to water vapour impact on the absorption
line shape was applied along with the Webb–Pearman–Leuning (WPL) dilution
correction due to water vapour on high-frequency raw concentration output
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>X</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (mixing ratio with respect to moist air, uncorrected for
spectroscopic effect) according to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">χ</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msub><mml:mi>X</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:mo>(</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:mi>b</mml:mi><mml:mo>)</mml:mo><mml:msub><mml:mi mathvariant="italic">χ</mml:mi><mml:mi mathvariant="normal">V</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mrow></mml:math></inline-formula>. Here <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">χ</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">χ</mml:mi><mml:mi mathvariant="normal">V</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
are the instantaneous mixing ratios of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O and water vapour with respect
to dry air.  The spectroscopic correction coefficient <inline-formula><mml:math display="inline"><mml:mi>b</mml:mi></mml:math></inline-formula> was   determined
experimentally for each instrument (Table 1) by measuring the response of the
instrument (output <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>X</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) to sample air of standard gas (constant
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">χ</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) with varying water content <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">χ</mml:mi><mml:mi mathvariant="normal">V</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The
correction was not necessary for CS-TDL as a dryer installed after the air
intake point on the sampling line dried the air sample before the optical
cell. LGR-CW-QCL corrected for the water vapour effect using a built-in module
in the LGR data acquisition software; the same applied to AR-CW-QCL after a
software update in July 2011.</p>
      <p>Prior to calculating the turbulent fluxes, a 2-D rotation (mean lateral and
vertical wind equal to zero) of sonic anemometer wind components was done
according to Kaimal and Finnigan (1994) and all variables were linearly
de-trended. The EC fluxes were calculated as 30 min covariances between the
scalars and vertical wind velocity following commonly accepted procedures
(e.g. Aubinet et al., 2000). Time lag between the concentration and wind
measurements induced by the sampling lines was determined by maximizing the
covariance. For CS-TDL, the lag was determined by maximizing the covariance
for the high flux period only (day of year (DOY) 144–146) because in other
periods the lag was not well defined by using this method. The final
processing (instruments CS-TDL, AR-CW-QCL and LGR-CW-QCL) was done by fixing
the time lag to avoid unphysical variations of lag due to random
flux errors. For the AR-P-QCL system, the lag was determined by maximising the
covariance for CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, and the same lag was assigned to N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O. This was
to use the instrument's ability to also measure CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, therefore enabling the use of a much better signal-to-noise ratio for determinating lag
time. Spectral corrections were applied to account for the low- and high-frequency attenuation of the covariances (Sect. 2.4). Then, the humidity
effect on temperature flux was accounted for after Schotanus et al. (1983).
All data processing was performed with post-processing software EddyUH
(<uri>http://www.atm.helsinki.fi/Eddy_Covariance/EddyUHsoftware.php</uri>).</p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Spectral corrections</title>
      <p>Low- and high-frequency variations in the measured signal are attenuated due
to data acquisition and processing, and by a non-ideal measurement system
(e.g. Moore, 1986; Moncrieff et al., 1997; Rannik and Vesala, 1999; Massman,
2000). Block averaging and de-trending of data acts as a high-pass filter,
thus damping low-frequency changes (Rannik and Vesala, 1999; Finnigan
et al., 2003). Turbulent fluctuations occurring at high frequencies are
attenuated due to the measurement system's limitations. Gas analyser's
finite frequency response, attenuation of fluctuations in the sampling line,
spatial separation between the anemometer measurement head and sampling line
inlet affect the attenuation of high-frequency fluctuations in the signal.</p>
      <p>The observed flux (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi mathvariant="normal">m</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) can be formally presented as the integral
over the convolution of the true co-spectrum (Co, unaffected by frequency
attenuation) with the co-spectral transfer function as
            <disp-formula id="Ch1.E1" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi mathvariant="normal">m</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:munderover><mml:mo movablelimits="false">∫</mml:mo><mml:mn mathvariant="normal">0</mml:mn><mml:mi mathvariant="normal">∞</mml:mi></mml:munderover><mml:mi>T</mml:mi><mml:mo>(</mml:mo><mml:mi>f</mml:mi><mml:mo>)</mml:mo><mml:mi mathvariant="normal">Co</mml:mi><mml:mo>(</mml:mo><mml:mi>f</mml:mi><mml:mo>)</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>f</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where the co-spectral transfer function <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>T</mml:mi><mml:mo>(</mml:mo><mml:mi>f</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> can be presented as the convolution
of respective low-frequency <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">L</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:mi>f</mml:mi></mml:mrow></mml:math></inline-formula>) and high-frequency <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">H</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:mi>f</mml:mi></mml:mrow></mml:math></inline-formula>) transfer
functions. For details on the low-frequency transfer function due to high-pass filtering
and/or finite averaging period, see Rannik and Vesala (1999).</p>
      <p>For evaluation of the instrument frequency performance and subsequent
high-frequency flux corrections during post-processing, the high-frequency
transfer function of the EC system was estimated (Aubinet et al., 2000) as
the ratio of the observed and un-attenuated flux (Horst, 1997). The
co-spectral transfer function <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">H</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:mi>f</mml:mi></mml:mrow></mml:math></inline-formula>) for a system behaving as a first-order response sensor can be described by
            <disp-formula id="Ch1.E2" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">H</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:mi>f</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:mo>(</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi><mml:mi>f</mml:mi><mml:mi mathvariant="italic">τ</mml:mi><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math display="inline"><mml:mi>f</mml:mi></mml:math></inline-formula> is the natural frequency and <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">τ</mml:mi></mml:math></inline-formula> the (first-order) response
time of the attenuator (sensor or the system in total) (Horst, 1997). The
effective transfer function of the EC system for different instruments was
estimated as the ratio of co-spectral density of scalar flux relative to
co-spectrum of sensible heat flux (Aubinet et al., 2000). Such a
procedure assumed that temperature measurements were not affected by
attenuation (true for the sonic anemometer) and includes normalization with
integral over frequencies not affected by attenuation.</p>
</sec>
<sec id="Ch1.S2.SS5">
  <title>Estimation of random errors</title>
      <p>Turbulent fluxes averaged over a limited time period have random errors
because of the stochastic nature of turbulence (Lenschow et al., 1994; Rannik
et al., 2006) as well as due to noise presented in measured signals
(Lenschow and Kristensen, 1985).</p>
      <p>The random error of the flux was evaluated as 1 standard deviation of the
covariance error, hereafter in the manuscript denoted by <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. It
was defined through the variance of the distribution of the individual flux
realization around the ensemble mean (e.g. Lenschow et al., 1994).
Theoretically, there are several approaches to approximate the same error
estimate; see e.g. Rannik et al. (2009). Currently, the flux random error
was calculated according to the method implemented in EddyUH, the method
proposed by Finkelstein and Sims (2001). The method evaluates the error in
the time domain through integration of the auto-covariance and cross-covariance
functions of the vertical wind speed and the scalar concentration according
to
            <disp-formula id="Ch1.E3" content-type="numbered"><mml:math display="block"><mml:mrow><?xmltex \hack{\hbox\bgroup\fontsize{8.5}{8.5}\selectfont$\displaystyle}?><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:msub><mml:mo>≈</mml:mo><mml:msqrt><mml:mrow><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mi>n</mml:mi></mml:mfrac></mml:mstyle><mml:mfenced close="]" open="["><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mi>m</mml:mi></mml:mrow><mml:mi>m</mml:mi></mml:munderover><mml:mover accent="true"><mml:mrow><mml:msup><mml:mi>w</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msup><mml:mi>w</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow><mml:mo mathvariant="normal">‾</mml:mo></mml:mover><mml:mo>(</mml:mo><mml:mi>p</mml:mi><mml:mo>)</mml:mo><mml:mover accent="true"><mml:mrow><mml:msup><mml:mi>c</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msup><mml:mi>c</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow><mml:mo mathvariant="normal">‾</mml:mo></mml:mover><mml:mo>(</mml:mo><mml:mi>p</mml:mi><mml:mo>)</mml:mo><mml:mo>+</mml:mo><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mi>m</mml:mi></mml:mrow><mml:mi>m</mml:mi></mml:munderover><mml:mover accent="true"><mml:mrow><mml:msup><mml:mi>w</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msup><mml:mi>c</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow><mml:mo mathvariant="normal">‾</mml:mo></mml:mover><mml:mo>(</mml:mo><mml:mi>p</mml:mi><mml:mo>)</mml:mo><mml:mover accent="true"><mml:mrow><mml:msup><mml:mi>c</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msup><mml:mi>w</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow><mml:mo mathvariant="normal">‾</mml:mo></mml:mover><mml:mo>(</mml:mo><mml:mi>p</mml:mi><mml:mo>)</mml:mo></mml:mfenced></mml:mrow></mml:msqrt><mml:mo>,</mml:mo><?xmltex \hack{$\egroup}?></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math display="inline"><mml:mrow><mml:mover accent="true"><mml:mrow><mml:msup><mml:mi>w</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msup><mml:mi>w</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow><mml:mo mathvariant="normal">‾</mml:mo></mml:mover><mml:mo>(</mml:mo><mml:mi>p</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mn mathvariant="normal">1</mml:mn><mml:mi>n</mml:mi></mml:mfrac><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mrow><mml:mi>n</mml:mi><mml:mo>-</mml:mo><mml:mi>p</mml:mi></mml:mrow></mml:munderover><mml:mfenced close=")" open="("><mml:mi>w</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>-</mml:mo><mml:mover accent="true"><mml:mi>w</mml:mi><mml:mo mathvariant="normal">‾</mml:mo></mml:mover></mml:mfenced><mml:mfenced open="(" close=")"><mml:mi>w</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mi>p</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>-</mml:mo><mml:mover accent="true"><mml:mi>w</mml:mi><mml:mo mathvariant="normal">‾</mml:mo></mml:mover></mml:mfenced></mml:mrow></mml:math></inline-formula>.
In calculations, we used <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>m</mml:mi><mml:mo>=</mml:mo><mml:mn>200</mml:mn></mml:mrow></mml:math></inline-formula> (corresponding to 20 s) to ensure that
integration of the covariance functions was performed over times exceeding
the integral timescale of turbulence. This mathematically rigorous method
provides estimates for the random uncertainty of the flux measurements for
every flux averaging period.</p>
      <p>Random uncertainty of the observed covariance due to presence of noise in
instruments signal, giving essentially the lowest limit of the flux that the
system is able to measure, was expressed in its simplest form as
            <disp-formula id="Ch1.E4" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi mathvariant="normal">F</mml:mi><mml:mo>,</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">noise</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">w</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">noise</mml:mi></mml:msub></mml:mrow><mml:msqrt><mml:mrow><mml:mi>f</mml:mi><mml:mi>T</mml:mi></mml:mrow></mml:msqrt></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">w</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">noise</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> denote the standard deviation
of the turbulent record of vertical wind speed and the standard deviation of
instrumental noise as observed at frequency <inline-formula><mml:math display="inline"><mml:mi>f</mml:mi></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> denotes the flux averaging
period. The expression above assumes that the noise component of the
vertical wind speed measurement is negligible. In this study, we use the
method developed by Lenschow et al. (2000) and applied to EC fluxes by
Mauder et al. (2013) to estimate the flux error due to instrumental noise.
Lenschow et al. (2000) derived the method to estimate the instrumental
random noise variance <inline-formula><mml:math display="inline"><mml:mrow><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">noise</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> from the auto-covariance
function of the measured turbulent record close to zero-shift, enabling one to
determine the error for each half-hour flux averaging period.</p>
      <p>The random flux error <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the result of limited sampling in
time and/or in space of a stochastic turbulence realization. Its expression
includes the covariance and cross-covariance functions of turbulent records;
it therefore, in addition to variances and covariances, accounts for the
respective integral timescales of turbulent records. The error <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> also incorporates the contribution due to instrumental noise and is
therefore larger than <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi mathvariant="normal">F</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">noise</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>The error <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi mathvariant="normal">F</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">noise</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> instead does not depend on the integral timescale of turbulence; it is therefore mainly determined by the instrumental
noise characteristics and less by the observation conditions (only via
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">w</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>). Assuming no true turbulent variation of concentration and
thus zero flux, the calculated flux will be generally non-zero due to noise
in the instrumental signal. Evidently the system will not be able to detect the
fluxes smaller than the ones obtained from the expression for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi mathvariant="normal">F</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">noise</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Therefore, this is the minimum flux that the EC system can
detect and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi mathvariant="normal">F</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">noise</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> proves useful in characterising the
instrumental limitation to detect small fluxes.</p>
      <p>If an average over fluxes <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mi mathvariant="normal">…</mml:mi><mml:mi>N</mml:mi></mml:mrow></mml:math></inline-formula>) is calculated, each of
these representing a flux value observed over averaging period <inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> and being
characterized by an error <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi>F</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, then the error of the average flux
<inline-formula><mml:math display="inline"><mml:mrow><mml:mfenced close="〉" open="〈"><mml:mi>F</mml:mi></mml:mfenced><mml:mo>=</mml:mo><mml:mfrac><mml:mn mathvariant="normal">1</mml:mn><mml:mi>N</mml:mi></mml:mfrac><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mi>N</mml:mi></mml:msubsup><mml:msub><mml:mi>F</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
is expressed as
            <disp-formula id="Ch1.E5" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Δ</mml:mi><mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>F</mml:mi><mml:mo>&gt;</mml:mo></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msqrt><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mi>N</mml:mi></mml:msubsup><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mrow><mml:mi>F</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:msup><mml:mi>N</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle></mml:msqrt><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
          This expression will be used to estimate the random errors of the average
fluxes in Sect. 3.4.</p>
</sec>
<sec id="Ch1.S2.SS6">
  <title>Periods of analysis and quality screening</title>
      <p>The intercomparison measurements were performed from the beginning of the
growing season in April until November 2011. According to instrumental data
coverage, the period was divided into three sub-periods for the instrument
evaluation and flux analysis purposes. During period I, DOY 110–181
(20 April–30 June 2011), the measurements of CS-TDL, AR-CW-QCL and AR-P-QCL were
available; during period II, DOY 206–271 (25 July–28 September 2011), all
instruments were measuring; and during period III, DOY 272–324
(29 September–20 November 2011), all other except CS-TDL were operational. Prior to
analysis data quality screening was performed. The measurements corresponding
to wind direction interval 50–110<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> were excluded as possibly affected
by the instrumental cabin. In addition, quality screening was performed according
to Vickers and Mahrt (1997) by applying the following statistics and
selection thresholds: data with N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O concentration skewness outside (<inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>2,
2), kurtosis outside (1, 8) or Haar mean and Haar variance exceeding 3
were rejected. Applying the same statistics and thresholds as for N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O,
additional quality screening of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes was performed according to
H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O concentration statistics for AR-CW-QCL and AR-P-QCL due to the
impact of the spectroscopic and dilution corrections on fluxes and according
to CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> concentration statistics for AR-P-QCL because the lag obtained
for CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> was assigned to N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O in the case of this instrument.</p>
      <p>The applied quality criteria were used to ensure exclusion of the system
malfunctioning as well as unphysical and/or unusual occasions. No quality
screening for stationarity was performed as the focus of the study was the
instrumental intercomparison, which was not affected by occasional
non-stationary conditions included in the analysed data set.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
      <p>The fluxes obtained for three periods are presented in Fig. 1, being averaged
over daily period for the clarity of presentation. No gap-filling was used
and for each day only the existing measurements, after applying the data quality
screening described above, were averaged. In May, the fluxes increased
significantly after fertilization and then decreased back to a low,
although clearly positive, level after a few weeks. This was the only occasion
of high N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O emission followed by continuous decrease of fluxes towards
the autumn. The soil temperature had an increasing trend until about DOY 205
(24 July 2011) and since August declining seasonal trend (Fig. 2). Soil water content (SWC)
increased with occasional rain events. During the high emissions, starting
on DOY 144 (24 July 2011) and lasting until approximately DOY 155
(4 June 2011), the SWC was relatively high at approximately 0.3 m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>Daily average fluxes for four instruments containing period I DOY
110–181 <bold>(a)</bold>, period II DOY 206–271 <bold>(b)</bold> and period III DOY 272–324 <bold>(c)</bold>. No
gap-filling was used in the calculation of daily average fluxes.</p></caption>
        <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f01.pdf"/>

      </fig>

      <p>The high fluxes observed during that period enable us to evaluate the
frequency performance of three systems including CS-TDL, AR-CW-QCL and
AR-P-QCL. The LGR-CW-QCL instrument was not operational then and the
frequency response analysis for this instrument was performed based on the
concurrently measured H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O and CO signal analysis.</p>
<sec id="Ch1.S3.SS1">
  <title>Spectral characteristics of the instruments</title>
      <p>Spectral analysis was performed to study the frequency performance of the
instruments. In general, averaging over long periods should lead to better
spectral statistics. However, aggregating over different periods might lead
to biased results as the spectra do not necessary follow the idealized
normalizations in frequency scale, considering also that spectral scaling
depends on stability. Therefore, we aimed to use optimal averaging period over
several hours for similar conditions in terms of wind speed and stability.
For the period of 26 May from 7:00 to 13:00 EET (eastern European time) when
the conditions were moderately unstable (average wind speed of the
period 3.2 m s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and sensible heat flux 50 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), the
calculated spectra exhibited very clear and systematic patterns for
temperature as well as N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O concentration records measured by the three
instruments (Fig. 3). In spite of high fluxes registered by the instruments
during this period, the CS-TDL N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O signal was dominated by noise almost over
the whole frequency range presented. For AR-CW-QCL, almost no evidence of
noise could be observed in the power spectral plot (multiplied with
frequency). The older Aerodyne instrument, the AR-P-QCL, revealed an
increase of the spectral density only at the high-frequency end of the power
spectrum, characteristic of noise contribution. The co-spectra of
all three instruments showed smooth patterns, the shape being consistent with
the co-spectral model by Kaimal et al. (1972) but slightly shifted in
frequency scale. At the high-frequency ends of the presented co-spectra the
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O signal curves deviate from the theoretical as well as from
temperature co-spectra, indicating attenuation of signals at high frequencies
by the measurement systems.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p>Soil water content (SWC) at 2.5 cm depth and precipitation <bold>(a)</bold> and
soil temperature at 2.5 cm depth <bold>(b)</bold> during the measurement campaign.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f02.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p>Normalized co-spectra (left panels) and spectra (right panels) of
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O measurements by instruments CS-TDL <bold>(a, b)</bold>, AR-CW-QCL
<bold>(c, d)</bold> and AR-P-QCL <bold>(e, f)</bold> during the high flux
period, DOY 146 (26 May 2011) 7:00 to 13:00 EET. The RCG crop was about 0.4 m
tall during the given period.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f03.pdf"/>

        </fig>

      <p>The same time period was used to estimate the frequency response of the
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O eddy covariance systems according to the method described in
Sect. 2.4 (Fig. 4). The time constants estimated by making use of the
co-spectra presented in Fig. 3 and Eq. (2) for CS-TDL, AR-CW-QCL and AR-P-QCL
were 0.12, 0.07 and 0.08 s, respectively. Note that these time
constants characterise the frequency response of the systems in total.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>Co-spectral transfer functions derived for CS-TDL <bold>(a)</bold>, AR-CW-QCL
<bold>(b)</bold> and AR-P-QCL <bold>(c)</bold> from the temperature and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O co-spectra presented
in Fig. 2.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f04.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p>Normalized co-spectra (left panels) and spectra (right panels) of
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O measurements by instruments AR-CW-QCL <bold>(a, b)</bold> and
LGR-CW-QCL <bold>(c, d)</bold> during the period DOY 216 (4 August 2011) 00:30
to 4:00 EET. The RCG crop was about 1.8 m tall during the given period.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f05.pdf"/>

        </fig>

      <p>Although the response time obtained for the AR-P-QCL system from high flux
period was 0.08 s, the analysis of the response time from measured
CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> signal for several other periods yielded the average response time
0.15 s. The N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O signal was synchronized with CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> by using the
lag determined for CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and theoretically the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O response time
does not differ from that of CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> under turbulent tube flow regime;
hence we choose the constant value 0.15 s for co-spectral corrections
throughout the campaign for this instrument.</p>
      <p>Spectral analysis was also performed for the period when LGR-CW-QCL
measurements were available. For comparison purposes, the results of the
time period of 4 August from 00:30 to 4:00 EET are presented for AR-CW-QCL
and LGR-CW-QCL instruments (Fig. 5). The period was chosen with relatively
high fluxes (with LGR-CW-QCL measurements available) and similar stability
and wind conditions (average wind speed of the period of 0.94 m s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and
sensible heat flux of <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>37.5 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). The power spectra of both
instruments revealed a contribution of noise at the high-frequency end of the
spectra, which was more pronounced for LGR-CW-QCL. The co-spectra were more
scattered when compared to high flux period (Fig. 3). Estimation of the
frequency response of the systems based on this period was uncertain due to
scatter and could not be used as the basis for co-spectral corrections for
LGR-CW-QCL.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6"><caption><p><bold>(a)</bold> Instrumental noise, presented as 1 standard deviation of the
noise at 10 Hz frequency, <bold>(b)</bold> N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O flux random error (blue) and flux
random error due to instrumental noise (green) statistics; <bold>(c)</bold> the same as
<bold>(b)</bold> but for relative fluxes. The boxplots present the lower and upper
percentiles, quartiles and median values of the distributions. Based on flux
measurements during the period DOY 206–271 (period II).</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f06.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7"><caption><p>Correlation scatter plots of 30 min average N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes (in
nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), as measured by CS-TDL and AR-P-QCL vs. AR-CW-QCL
during period I DOY 110–181 <bold>(a, b)</bold>, and CS-TDL and
LGR-CW-QCL vs. AR-CW-QCL during period II DOY 206–271 <bold>(c, d)</bold>. The lines present the linear fit with coefficients presented on the
plots.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f07.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8"><caption><p>Cumulative sums of available flux data for three periods:  <bold>(a)</bold> period I DOY 110–181 (20 April–30 June 2011),  <bold>(b)</bold> period
II DOY 206–271 (25 July–28 September 2011) and <bold>(c)</bold> period III DOY 272–324
(29 September–20 November 2011). Accumulation of fluxes for each instrument was performed
only for data if measurements were available for all instruments used in
respective period. No gap filling was used.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://www.biogeosciences.net/12/415/2015/bg-12-415-2015-f08.pdf"/>

        </fig>

      <p>The main difference in the flow set-ups of the systems concerned LGR-CW-QCL.
With a larger tube diameter and slightly lower flow rate, the flow regime was
likely laminar (Re <inline-formula><mml:math display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn>2000</mml:mn></mml:mrow></mml:math></inline-formula>), whereas for other instruments it was
clearly turbulent (Re <inline-formula><mml:math display="inline"><mml:mrow><mml:mo>≥</mml:mo><mml:mn>4600</mml:mn></mml:mrow></mml:math></inline-formula>). It is well established that under laminar
flow regime tube flow attenuates turbulent fluctuations of concentration much
more than under turbulent flow. According to the expression for tube
attenuation in laminar flow regime (Foken et al., 2012) the first-order
response time for LGR-CW-QCL flow set-up would be 0.37 s (estimated for
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O). For turbulent flow (ARI-CW-QCL set-up) the theoretical response
time for tube damping is much smaller (0.01 s) than the response time
obtained from the co-spectra (0.07 s), suggesting that the system's response
was dominated by the instrumental response.</p>
      <p>The frequency response of the LGR-CW-QCL system was further determined from
the co-spectral analysis of the CO signal, and we obtained the value of 0.26 s.
We also determined the experimental response time for water vapour from
several periods corresponding to low-humidity conditions (RH &lt; 40 %) and we consistently found the value around 0.35 s (for LGR-CW-QCL
system). For comparison, the response time for H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O measured by the
ARI-CW-QCL system was determined to be 0.10 s. Damping of water fluctuations
in sampling lines is stronger than for other scalars as evidenced by
experimental studies (e.g. Mammarella et al., 2009). This is due to
adsorption/desorption of water molecules on tube walls. This explains the
difference between the response times obtained from CO and H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O. Thus, we
believe that a value of 0.26 s characterises well the <?xmltex \hack{\mbox\bgroup}?>first-order<?xmltex \hack{\egroup}?> response
time of the LGR-CW-QCL set-up for N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O, and we use this value in co-spectral
corrections. Note, however, that a higher response time of the LGR-CW-QCL
system does not mean a slower instrument performance because the system has
more damping primarily in the sampling line due to a lower flow rate and larger
tube diameter (Table 2).</p>
      <p>The frequency response times determined in this section were used in
performing the co-spectral corrections (Table 2) as described in Sect. 2.4;
the typical magnitudes of these corrections are presented in Table 3.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3"><caption><p>Statistics of spectral corrections of fluxes as percentage of raw
uncorrected fluxes: lower percentile/median/upper percentile. Based on flux
measurements during the period DOY 206–271 (period II) and data classified as
qualified (Table 4). Daytime was defined by the elevation of sun higher than
zero and night-time lower than zero, respectively. Statistics were derived
for data when measurements were available for all four instruments.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.78}[.78]?><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">CS-TDL</oasis:entry>  
         <oasis:entry colname="col3">AR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col4">LGR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col5">AR-P-QCL</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">All data</oasis:entry>  
         <oasis:entry colname="col2">4.0/6.2/10.2</oasis:entry>  
         <oasis:entry colname="col3">2.4/3.6/6.0</oasis:entry>  
         <oasis:entry colname="col4">6.9/12.3/20.0</oasis:entry>  
         <oasis:entry colname="col5">4.5/7.3/14.8</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Daytime data</oasis:entry>  
         <oasis:entry colname="col2">4.0/6.1/9.8</oasis:entry>  
         <oasis:entry colname="col3">2.6/3.6/5.8</oasis:entry>  
         <oasis:entry colname="col4">6.9/12.0/18.5</oasis:entry>  
         <oasis:entry colname="col5">4.5/6.9/10.5</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Night data</oasis:entry>  
         <oasis:entry colname="col2">3.6/6.3/11.3</oasis:entry>  
         <oasis:entry colname="col3">2.2/3.6/6.4</oasis:entry>  
         <oasis:entry colname="col4">6.7/12.9/22.3</oasis:entry>  
         <oasis:entry colname="col5">4.5/7.7/20.2</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S3.SS2">
  <title>Random uncertainty of fluxes and instrumental noise</title>
      <p>The method by Lenschow et al. (2000) described in Sect. 2.5 enables the
calculation of the instrumental noise for each 30 min period and the resulting
flux uncertainty due to instrumental noise. Figure 6a shows the estimated
signal's noise statistics with upper and lower percentiles and quantiles
(boxes), with a median value in the middle. For all instruments except
LGR-CW-QCL, the distributions are very narrow and different percentiles cannot
be separated from the plot (for values see Table 1). This tells us that the
noise levels of the three instruments are very stable, but the noise level of
LGR-CW-QCL somewhat varies. In a comparison of the instruments, AR-CW-QCL has
by far the lowest noise level of around 0.12 ppb (standard deviation of the
signal's noise at 10 Hz frequency). The two instruments, LGR-CW-QCL and
AR-P-QCL, are characterized by a similar noise level (around 0.5 ppb), while
CS-TDL signals show the highest noise level (2 ppb). Consequently, these
instrumental noise levels are reflected in the random errors of fluxes,
determining essentially the minimum flux level that each instrument is able
to measure at a given flux averaging interval (30 min period). For
AR-CW-QCL, the respective lowest flux is around 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (as
given by median in Fig. 6b), for LGR-CW-QCL and AR-P-QCL around
4 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and for CS-TDL
0.15 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p>
      <p>The frequency distributions of the total flux random errors, calculated
according to Eq. (3), are naturally higher than the flux error due to
instrumental noise only. It can be observed that in the case of full flux random
error, the difference between different instruments is reduced (Fig. 6b)
because in addition to instrumental noise impact, this error statistic also
incorporates the flux uncertainty due to the stochastic nature of turbulence. The
relative random errors (Fig. 6c) are the largest for CS-TDL (being of the
order of 100 % and in most cases less than <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>300 %) and the
smallest for AR-CW-QCL instruments (median around 30 % and the error mostly
less than 100 %). It is the signal's noise of the instrument
that contributes to the random error of the flux, determining which
instrument is able to detect the lowest fluxes. In the case of CS-TDL the
low-frequency signal drifting can also enlarge the total random error of the
calculated flux.</p>
</sec>
<sec id="Ch1.S3.SS3">
  <title>Intercomparison of fluxes averaged over turbulent spectrum</title>
      <p>It was observed that the fluxes calculated from CS-TDL measurements during
the low flux period were dominated by stochastic uncertainty, being
frequently of the order of the random uncertainties of the fluxes (Sect. 3.2).
Therefore, the fluxes averaged over the 30 min period were compared for this
instrument with AR-CW-QCL results over the period DOY 110–182, which
included the high emissions episode starting on DOY 144 and exhibiting
elevated fluxes until approximately DOY 155. In general, the fluxes with high
magnitudes obtained by CS-TDL compared well with those of obtained by
AR-CW-QCL (Fig. 7a). The AR-P-QCL system, as compared with AR-CW-QCL, showed
systematically lower fluxes during the given period of high fluxes (slope
0.70). In spite of the lower noise level of this instrument, the coefficient of
determination for this instrument (0.63) was lower than that for CS-TDL
(0.77) in comparison to the fluxes as measured by AR-CW-QCL.</p>
      <p>During the second observation period, when fluxes were much lower, CS-TDL was
not able to determine fluxes with sufficiently small error and the
correlation with AR-CW-QCL at the 30 min averaging level was very low (Fig. 7c).
At around zero fluxes as measured by AR-CW-QCL, the results of CS-TDL showed
scattered values visually between <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>2 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. The noise
level of CS-TDL around 2 ppb translates into a flux uncertainty due to
instrumental noise of about 0.05 to 0.3 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. The total
flux error <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was within the range of 0.1 to
0.45 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (upper and lower quantiles of the distribution
in Fig. 6b). We analysed the range of variation of CS-TDL fluxes during the
given period DOY 206–272, conditionally selecting the observations when the
observed fluxes by AR-CW-QCL were absolutely smaller than
0.15 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (90 % of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O flux random errors for
AR-CW-QCL less than this value during the given period). The respective
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes as determined by CS-TDL were characterized by the upper and
lower quantiles of <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.27 and 0.52 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. This is
consistent with the upper quantile of the flux error distribution for CS-TDL.
Therefore, the fluxes of CS-TDL, corresponding to close-to-zero fluxes as
determined by AR-CW-QCL, were consistent with the flux error estimates.</p>
      <p>The comparison of the 30 min average fluxes calculated from two instruments,
AR-CW-QCL and LGR-CW-QCL, revealed very good correspondence and high
correlation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn>0.90</mml:mn></mml:mrow></mml:math></inline-formula>) even though those measurements corresponded to
very low N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes. The slope close to unity and a negligible intercept
indicates that there is no systematic bias between the measurements of these systems
(Fig. 7d).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T4" specific-use="star"><caption><p>Average fluxes (nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>random error of the
average. Period I DOY 110–181 (20 April–30 June 2011), period II DOY 206–271
(25 July–28 September 2011), period III DOY 272–324 (29 September–20 November 2011). Percent data
available represents the fraction of half-hour periods when data from all
instruments (three in periods I and III and all four in period II) was available (data from wind direction interval
50–110<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> excluded), relative to full time period length. Averaging of
fluxes for each instrument was performed only for data if measurements were
available for all instruments used in respective period. No gap filling was
used.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="8">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="center"/>
     <oasis:colspec colnum="3" colname="col3" align="center"/>
     <oasis:colspec colnum="4" colname="col4" align="center"/>
     <oasis:colspec colnum="5" colname="col5" align="center"/>
     <oasis:colspec colnum="6" colname="col6" align="center"/>
     <oasis:colspec colnum="7" colname="col7" align="center"/>
     <oasis:colspec colnum="8" colname="col8" align="center"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">% data</oasis:entry>  
         <oasis:entry colname="col3">% data qualified</oasis:entry>  
         <oasis:entry colname="col4">no. of 30 min periods</oasis:entry>  
         <oasis:entry colname="col5">CS-TDL</oasis:entry>  
         <oasis:entry colname="col6">AR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col7">LGR-CW-QCL</oasis:entry>  
         <oasis:entry colname="col8">AR-P-QCL</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">available</oasis:entry>  
         <oasis:entry colname="col3">(out of available)</oasis:entry>  
         <oasis:entry colname="col4">averaged</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Period I</oasis:entry>  
         <oasis:entry colname="col2">69.2</oasis:entry>  
         <oasis:entry colname="col3">75.2</oasis:entry>  
         <oasis:entry colname="col4">1797</oasis:entry>  
         <oasis:entry colname="col5">0.931 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.018</oasis:entry>  
         <oasis:entry colname="col6">0.870 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.009</oasis:entry>  
         <oasis:entry colname="col7">–</oasis:entry>  
         <oasis:entry colname="col8">0.560 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.011</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Period II</oasis:entry>  
         <oasis:entry colname="col2">55.0</oasis:entry>  
         <oasis:entry colname="col3">79.4</oasis:entry>  
         <oasis:entry colname="col4">1383</oasis:entry>  
         <oasis:entry colname="col5">0.183 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.010</oasis:entry>  
         <oasis:entry colname="col6">0.146 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.006</oasis:entry>  
         <oasis:entry colname="col7">0.138 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.007</oasis:entry>  
         <oasis:entry colname="col8">0.124 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.003</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Period III</oasis:entry>  
         <oasis:entry colname="col2">61.4</oasis:entry>  
         <oasis:entry colname="col3">78.2</oasis:entry>  
         <oasis:entry colname="col4">1220</oasis:entry>  
         <oasis:entry colname="col5">–</oasis:entry>  
         <oasis:entry colname="col6">0.067 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.002</oasis:entry>  
         <oasis:entry colname="col7">0.057 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.002</oasis:entry>  
         <oasis:entry colname="col8">0.058 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.003</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S3.SS4">
  <title>Long-term averages and systematic differences</title>
      <p>In order to evaluate the possible systematic differences, cumulative curves
of the flux observations were calculated. No gap-filling of missing data was
done, but instead only the half-hour periods were used when the results for
all instruments were available. Thus, the cumulative sums are not assumed to
represent the total emissions over the given periods, although rough
estimates could be calculated by using the data coverage percentages presented in Table 4 to account for missing flux data. The summation of fluxes over the
first and second periods reveals that CS-TDL gives the highest flux sums and
AR-P-QCL the lowest, in particular during the first period (Fig. 8). The
cumulative sums for fluxes obtained from AR-CW-QCL and LGR-CW-QCL
measurements converge over periods II and III and show only small differences.
Also, the cumulative fluxes measured by AR-P-QCL during these periods are very
close to fluxes measured by the two other instruments. In order to assess the
magnitude of the random errors in these differences, the random errors of the
fluxes averaged over the three periods were calculated according to Eq. (5). The
analysis revealed that the average fluxes for period II, obtained from the
measurements of AR-CW-QCL and LGR-CW-QCL instruments, did not differ within
calculated error limits, and were very close during period III to the
result for AR-P-QCL (Table 4).</p>
      <p>However, CS-TDL produced a 7 % higher total sum for the period of high
fluxes (DOY 110–181 with an average flux of 0.87 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
as determined by AR-CW-QCL) and a 29 % higher sum for the second period
(DOY 206–271) compared to an average flux 0.142 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(average of AR-CW-QCL and LGR-CW-QCL results). The AR-P-QCL instrument
determined for these two periods 36 and 13 % lower average fluxes,
respectively. The possible reasons for this will be discussed in the next
section. For the third period, the results of AR-P-QCL did not differ much
from the results of the other two instruments.</p>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
      <p>Performance of four instruments (see Tables 1 and 2) capable of fast response
measurement of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O was studied throughout the 2011 growing season over a
field cultivated with RCG in eastern Finland. The N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes were small
in the beginning of the season, increased significantly after
fertilization (late May) and then decreased back to low, positive values
after a few weeks. Three instruments, CS-TDL, AR-CW-QCL and AR-P-QCL were
operational during this high emissions period. During this period, all
instruments detected the same flux dynamics, whereas the fluxes obtained by
AR-P-QCL, the previous instrument version by Aerodyne, were lower compared to
the other two instruments.</p>
      <p>For many applications, the systematic errors of micrometeorological flux
measurements of atmospheric trace gases are more important than the random
errors. For example, for determination of annual balances (e.g. Kroon et al.,
2010b) or for the comparison of exchange of different ecosystems (e.g.
Nicolini et al., 2013) the systematic errors become very important. The two
CW-QCL instruments compared very well on a half-hourly basis and produced
statistically close cumulative fluxes over the period when the two
instruments were simultaneously operational (25 July 2011–20 November 2011).
The cumulative emission estimate obtained by CS-TDL for period II (25 July–28 September 2011) was
29 % higher than the average result for instruments based on the
continuous-wave quantum cascade lasers, AR-CW-QCL and LGR-CW-QCL. AR-P-QCL
obtained 36 % lower fluxes than AR-CW-QCL during the first period
including the emission episode, whereas the correspondence with other
instruments during the rest of the campaign was relatively good.</p>
      <p>The systematic differences in fluxes could be the result of calibration
and/or limited stability of the system over time. The impact of the
instruments calibration (sensitivity shift) impact on flux systematic
differences can be assessed by using calibration information (Sect. 2.2) as
well as comparison of average concentrations measured by different
instruments. The two analysers based on CW-QCL-s are expected to be very
stable, which was confirmed by the measurements: the concentrations measured
by these two instruments were very consistent and the slope (characterising
sensitivity) of the 30 min average concentration comparison did not deviate
from unity by more than 5 % (with the coefficient of determination of
linear regression <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn>0.86</mml:mn></mml:mrow></mml:math></inline-formula>).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T5" specific-use="star"><caption><p>Average micrometeorological conditions during the experimental
periods. Period I DOY 110–181 (20 April–30 June 2011), period II DOY 206–271
(25 July–28 September 2011), period III DOY 272–324 (29 September–20 November 2011). Daytime
was defined by the elevation of sun higher than zero and night-time lower
than zero, respectively. Average latent heat fluxes were determined from IRGA
measurements.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="7">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="center"/>
     <oasis:colspec colnum="3" colname="col3" align="center"/>
     <oasis:colspec colnum="4" colname="col4" align="center"/>
     <oasis:colspec colnum="5" colname="col5" align="center"/>
     <oasis:colspec colnum="6" colname="col6" align="center"/>
     <oasis:colspec colnum="7" colname="col7" align="center"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Temperature</oasis:entry>  
         <oasis:entry colname="col3">Air rel.</oasis:entry>  
         <oasis:entry colname="col4">Wind   <?xmltex \hack{\hfill\break}?></oasis:entry>  
         <oasis:entry colname="col5">Friction</oasis:entry>  
         <oasis:entry colname="col6">Sensible</oasis:entry>  
         <oasis:entry colname="col7">Latent</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3">humidity,</oasis:entry>  
         <oasis:entry colname="col4">speed,</oasis:entry>  
         <oasis:entry colname="col5">velocity,</oasis:entry>  
         <oasis:entry colname="col6">heat flux,</oasis:entry>  
         <oasis:entry colname="col7">heat flux,</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3">%</oasis:entry>  
         <oasis:entry colname="col4">m s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">m s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6">W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col7">W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Day, I</oasis:entry>  
         <oasis:entry colname="col2">11.6</oasis:entry>  
         <oasis:entry colname="col3">62.9</oasis:entry>  
         <oasis:entry colname="col4">2.21</oasis:entry>  
         <oasis:entry colname="col5">0.28</oasis:entry>  
         <oasis:entry colname="col6">27.5</oasis:entry>  
         <oasis:entry colname="col7">78.9</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Night, I</oasis:entry>  
         <oasis:entry colname="col2">6.5</oasis:entry>  
         <oasis:entry colname="col3">78.3</oasis:entry>  
         <oasis:entry colname="col4">1.34</oasis:entry>  
         <oasis:entry colname="col5">0.14</oasis:entry>  
         <oasis:entry colname="col6"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>20.2</oasis:entry>  
         <oasis:entry colname="col7">8.1</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Day, II</oasis:entry>  
         <oasis:entry colname="col2">15.3</oasis:entry>  
         <oasis:entry colname="col3">75.2</oasis:entry>  
         <oasis:entry colname="col4">1.35</oasis:entry>  
         <oasis:entry colname="col5">0.26</oasis:entry>  
         <oasis:entry colname="col6">9.7</oasis:entry>  
         <oasis:entry colname="col7">109.3</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Night, II</oasis:entry>  
         <oasis:entry colname="col2">11.2</oasis:entry>  
         <oasis:entry colname="col3">90.3</oasis:entry>  
         <oasis:entry colname="col4">1.06</oasis:entry>  
         <oasis:entry colname="col5">0.17</oasis:entry>  
         <oasis:entry colname="col6"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>18.6</oasis:entry>  
         <oasis:entry colname="col7">10.1</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Day, III</oasis:entry>  
         <oasis:entry colname="col2">6.1</oasis:entry>  
         <oasis:entry colname="col3">85.0</oasis:entry>  
         <oasis:entry colname="col4">1.46</oasis:entry>  
         <oasis:entry colname="col5">0.29</oasis:entry>  
         <oasis:entry colname="col6"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>10.8</oasis:entry>  
         <oasis:entry colname="col7">41.5</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Night, III</oasis:entry>  
         <oasis:entry colname="col2">4.8</oasis:entry>  
         <oasis:entry colname="col3">90.6</oasis:entry>  
         <oasis:entry colname="col4">1.21</oasis:entry>  
         <oasis:entry colname="col5">0.23</oasis:entry>  
         <oasis:entry colname="col6"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>23.5</oasis:entry>  
         <oasis:entry colname="col7">11.5</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p>The sensitivity of AR-P-QCL did not change more than 6.1 % between
consecutive calibrations, and this can be considered as the maximum flux error
arising from the calibration accuracy of this instrument (Sec. 2.2).
Nevertheless, the correlation of the 30 min average concentration measured
by this instrument as compared to AR-CW-QCL was not as good (for the period
DOY 206–272, a slope of 1.05 was determined with <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn>0.63</mml:mn></mml:mrow></mml:math></inline-formula>). The
concentration comparison presented here does not imply that the calibration
bias was the reason for the observed flux systematic difference for the
instrument AR-P-QCL.</p>
      <p>The analyser CS-TDL is known for its signal drifting as illustrated and
discussed by Mammarella et al. (2010), and the absolute concentrations were
not well determined during our campaign. Therefore, accurate measurement of
absolute concentration by this instrument over a long period of time cannot
be expected, and the concentration comparison was not used as the method for
evaluation of the instrument's calibration impact on flux systematic bias.
Note that signal drifting makes the time series produced by the instrument
essentially non-stationary and therefore enhances the random variability of
the flux estimate around the true value. However, such enhanced random
uncertainty does not systematically affect the cumulative sums over longer
periods.</p>
      <p>In the case of low fluxes the water vapour dilution and spectral line broadening
effects are the primary suspects for the reasons in systematic differences
in fluxes (e.g. Peltola et al., 2014). Close correspondence of the
concentrations and fluxes as measured by AR-CW-QCL and LGR-CW-QCL let us
conclude that the spectroscopic and water vapour dilution corrections for
these instruments were adequate. Note that those corrections were done by
built-in functionality in the case of LGR-CW-QCL. For AR-CW-QCL, the respective
corrections were done in post-processing phase for period I and by
built-in software for the rest of the campaign.</p>
      <p>The only evident systematic flux error source that could affect performance
of CS-TDL would be incomplete drying of sample air. If that was the case,
then the calculated fluxes would have suffered from missing partial density and
spectroscopic corrections. Since the water fluxes are dominantly upward, a
respective correction would tend to increase the flux values, therefore
increasing even more the systematic difference relative to other
instruments.</p>
      <p>The instrument ARI-P-QCL is based on the pulsed quantum cascade laser. For
this instrument, the experimentally determined spectroscopic correction
coefficient was much lower than the coefficient for AR-CW-QCL (Table 1). The
reason for systematically lower values of fluxes determined by AR-P-QCL from
the beginning of the experiment in April until June 2011, but subsequent
relatively good comparison with other instruments towards the end of the
experiment in November 2011, is not known. Two types of corrections were
applied to N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes: the spectroscopic correction to account for the
impact of water vapour on the absorption line shape, and the co-spectral
correction. The latter correction was comparable to all instruments (Table 3)
and does not introduce a significant difference between instruments. The
spectroscopic correction was applied together with the water vapour dilution
correction (Sect. 2.3) and can constitute a major correction depending on the
value of the coefficient <inline-formula><mml:math display="inline"><mml:mi>b</mml:mi></mml:math></inline-formula>. The correction is related to the water vapour
flux, which was during the daytime on the average around 100 Wm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(periods I and II, Table 5), with mid-day averages around 150 to
200 Wm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Considering an average concentration of N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O around
330 ppb and spectroscopic correction value <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>b</mml:mi><mml:mo>=</mml:mo><mml:mn>0.39</mml:mn></mml:mrow></mml:math></inline-formula> (the value for
AR-CW-QCL), the spectroscopic correction can be a few tenths of
nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> during mid-day, which is of the order of the flux
magnitude. We used all auxiliary data available to investigate the possible
reasons for the systematic differences, but found no explaining variable or
reason. In particular, no systematic variation of the residual between
AR-P-QCL and AR-CW-QCL fluxes was found over wide range of latent heat fluxes
from <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>20 to 250 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. This proves that the dilution and
spectroscopic corrections were properly accounted for. In addition, larger
spectroscopic correction would not explain the systematic difference observed
only during the first period.</p>
      <p>Thus the reasons for flux underestimation by AR-P-QCL during period I
are not known, and we suggest that extreme care should be exercised during
long-term measurement campaigns both with N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O and H<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
calibrations due to the strong impact of the water vapour on the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O flux
through spectroscopic and dilution corrections.</p>
      <p>A comment should be made regarding the observation level used in the study.
When RCG was grown high, the measurement level was only about 0.5 m above
the canopy top. The measurements within the roughness sublayer can be
disturbed in terms of several statistics, but the impact can be expected to
reveal more in spectral shapes than in integral statistics. The spectra
obtained for N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O (Figs. 3 and 5) were dominated by white noise over
wider (CS-TDL) or narrow (AR-CW-QCL) frequency ranges depending on the
instrument in question. The temperature spectra were similarly affected by
the noise but only at the high-frequency end of spectra and we believe do
not show evidence of a canopy impact on spectral shapes. We checked also the
spectra for vertical wind speed (not shown). The spectra exhibited smooth and
consistent shapes, without the particular impact of the canopy foliage on
spectral forms usually observed inside canopies. Launiainen et al. (2007)
studied the turbulence statistics and spectral shapes within pine forest
canopy. They did not observe deviation of spectral shapes above canopy at
height <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>z</mml:mi><mml:mo>/</mml:mo><mml:mi>h</mml:mi><mml:mo>=</mml:mo><mml:mn>1.47</mml:mn></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi>h</mml:mi></mml:math></inline-formula> being the canopy height) from the atmospheric
surface layer forms; within the crown space (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>z</mml:mi><mml:mo>/</mml:mo><mml:mi>h</mml:mi><mml:mo>=</mml:mo><mml:mn>0.78</mml:mn></mml:mrow></mml:math></inline-formula>), the spectra
deviated only slightly from the above-canopy forms. Within the trunk space
(<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>z</mml:mi><mml:mo>/</mml:mo><mml:mi>h</mml:mi><mml:mo>=</mml:mo><mml:mn>0.4</mml:mn></mml:mrow></mml:math></inline-formula>), the spectra were distorted due to the drag imposed by the
canopy elements. This supports that the spectra measured close to but above
canopy are weakly affected by the canopy presence. Thus, we do not expect that
the relatively low observation level biases the overall N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O flux
magnitude
and that the comparison of instrumentation is affected. Also, the effect on
the instrumental noise and flux random uncertainty analysis is expected to be
very limited through the influence on the covariance functions. The positive
impact of the close positioning of the system could be its higher sensitivity
in detecting the low fluxes through higher concentration fluctuations
expected (more) close to the source level.</p>
      <p>Important characteristics of the instruments for performing the EC
measurements are the response time and the noise level. The response times
for CS-TDL, AR-CW-QCL and AR-P-QCL flux measurements systems were determined
to be 0.12 and 0.07 and 0.08 s, respectively. The main factors affecting the
response time of the closed-path EC system are the damping of fluctuations in
the sampling line and the instrumental response. Since the flow rate of the
CS-TDL system was higher, it can be concluded that the response
characteristics of other two instruments are superior. The response time of
the EC system including LGR-CW-QCL was larger due to the laminar tube flow
regime, but the instrumental response was not determined based on the current
field measurements.</p>
      <p>In order to understand drivers of exchange and infer the broad average
fluxes such as seasonal or annual sums by using gap-filling
methodologies, it is important that the exchange at a shorter timescale is
distinguishable from random variation. Therefore, an understanding of random
errors is important when working with low fluxes as is frequently the case
with N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O. At the half-hour averaging timescale, the flux estimates for
AR-CW-QCL and LGR-CW-QCL instruments were very well correlated and showed
good correspondence. Apart from high N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes exceeding a few
nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> during the high emissions period, CS-TDL was not able
to resolve the emission fluxes at half-hourly timescale. Therefore, one can
conclude that CS-TDL is not suitable for measuring such low fluxes if the aim
is to resolve fluxes at hourly timescale and not the daily or longer
averages.</p>
      <p>Aerodyne AR-CW-QCL had the lowest noise level (around 0.12 ppb at 10 Hz
sampling rate) compared to Los Gatos LGR-CW-QCL instrument (SD of noise
0.60 ppb) and has therefore an advantage in resolving low fluxes over short
averaging periods. The noise level of AR-P-QCL was comparable to LGR-CW-QCL, but the old-generation instrument Campbell CS-TDL suffered clearly
from higher noise level (around 2 ppb). Huang et al. (2014) reported for the
instrument similar to AR-CW-QCL the precision 0.066 ppb for 10 Hz. The
value obtained by us was higher roughly by a factor of 2. According to the
manufacturer, the precision of LGR-CW-QCL is 0.1 ppb at 1 Hz averaging; at
10 Hz this would correspond to 0.32 ppb. We have determined again a median
value roughly twice higher than this. Kroon et al. (2007) reported for the
instrument similar to AR-P-QCL the precision value of 0.5 ppb Hz<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(equivalent to 1.6 ppb at 10 Hz), whereas Neftel et al. (2007) and Eugster
et al. (2007) report 0.3 ppb Hz<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>(equivalent to 0.95 ppb at
10 Hz). Pihlatie et al. (2005) and Wang et al. (2013) report noise for
CS-TDL as 1 ppb and 1.5 ppb (at 10 Hz), respectively. Under field
conditions the instrumental noise can be somewhat higher compared to
laboratory conditions where the instrumental characteristics are typically
studied. Also, the estimation method from the field records where the
turbulent variation is superimposed by the instrumental noise can introduce
some uncertainty. In summary, the observed instrumental noise characteristics
for instruments compare well with the results reported by others and are
useful in characterising instrumental performance.</p>
      <p>The flux errors due to instrumental noise for the observation conditions
prevailing at the site were determined to be around
10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for AR-CW-QCL,
4 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for LGR-CW-QCL and AR-P-QCL and
0.15 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for CS-TDL. Based on a half-hour and
long-term flux comparison, the best correspondence was observed between the
systems with the new-generation instruments AR-CW-QCL and LGR-CW-QCL, of which
the former has the advantage of detecting lower fluxes at a half-hourly
averaging basis (lower noise level).</p>
      <p>The signal's noise of the anemometer used by the UH (USA1 by METEK) was
determined to be 0.037 m s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> at 10 Hz sampling frequency for the vertical
wind speed component. The noise level of the anemometer employed by the UEF
was similar. The flux error due to anemometer's noise for the observation
conditions prevailing at the site during the period DOY 206–271 (the period
for the statistics presented in Fig. 6) was determined to be around
2 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (the median value). This was
much less than the respective flux error around
10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for the instrument AR-CW-QCL, which had
the lowest noise level 0.012 ppb (median value) of all instruments compared.
Therefore, the assumption that the anemometer's noise affects flux detection
much less than the gas analysers was well justified.</p>
      <p>The chamber techniques are widely used to measure the soil N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O exchange.
The traditional way to perform chamber measurements is to determine the gas
concentration at several moments during the chamber operation (called
deployment time, DT). In such data collection the sources of uncertainty are
the imprecision related to gas sampling (either manual or automatic) as well
as instrumental uncertainty (e.g. Venterea et al., 2009), leading to a
measurement precision which is called the detection limit of chamber-based flux
measurement system. Neftel et al. (2007) report a flux detection limit of
about 0.23 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for their chamber system with DT of 10 min and the concentration sampling interval of 1 min. The measurement cycle
of the system was however 2 h. Wang et al. (2013) found for their
automatic and manual chamber systems detection limits of about
5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (0.05 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) for
hourly DT. Their instrument precision was high, around 0.4 % relative to
ambient N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O concentration. By using the methodology and scaled results
presented by Parkin et al. (2012), we estimated the flux detection limit of a
chamber system with an assumed chamber height of 0.5 m, area of
0.25 m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>, deployment time 30 min and instrumental precision as high as
0.1 % to be 0.03 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. It has to be noted that the
flux detection limit of the chamber systems depends on several factors such
as the type of the chamber and respective sampling method, the precision of
the instrument, chamber dimensions and operation time (DT). Nevertheless, the
obtained result is well comparable with the EC systems. The random error of
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes for 30 min averaging time for the instrument with lowest
noise, the AR-CW-QCL instrument, was found to be
0.036 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (the median value). Note that here we compare
the flux detection limit of the chamber-based systems (which accounts for all
possible sources of uncertainty) with the total stochastic error of the EC
fluxes. The results are of the same magnitude.</p>
      <p>In this study we followed the methodology proposed by Mauder et al. (2013) in
quantification of the random errors in EC fluxes, i.e. the stochastic error
and the error due to instrumental noise in flux. The relative random errors
obtained in our study were much larger than the respective errors reported by
Mauder et al. (2013) for CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> measurements, evidencing that the
importance of random errors depends on the trace gas of interest via
instrumental precision and the flux magnitude ratio. Kroon et al. (2010a)
focus on the evaluation of the EC flux measurements of CH<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
specifically. They observed over a dairy farm site the fluxes in the range of
15 to 110 ng N m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (0.5 to 4 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>),
which they classified in low to high flux classes. They performed
calibration of the instrument similar to our AR-P-QCL weekly and considered
the respective uncertainty random over longer periods of time. Kroon et
al. (2010a) reported the average daily and monthly flux relative
uncertainties of 31 and 7 %, respectively. In our study the N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
fluxes were typically much smaller (excluding the fertilization episode),
around 0.1 to 0.3 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. We measured with the similar
instrument 36 % lower fluxes than obtained by AR-CW-QCL over the period
DOY 110–181 and 13 % lower fluxes than obtained by two new-generation
instruments over the period DOY 206–271. Evidently our measurements
performance was affected by an unidentified error source, systematic in
nature. In evaluation of the annual balances of CH<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O fluxes
over a managed fen meadow, Kroon et al. (2010b) made an assumption that the
uncertainty in EC fluxes was random and was neglected in the evaluation of long-term averages. In our results, this assumption was contradicted, and we suggest
that all possible systematic error sources should be considered very
carefully in planning, implementing and evaluating the flux measurements of
trace gases.</p>
      <p>In analysing the random errors of the fluxes Kroon et al. (2010a) assumed
that the flux error due to instrumental precision in concentration
measurement was negligible. We observed that this was not necessarily the
case for N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O when low flux levels were measured and demonstrated that
the method originally proposed by Lenchow et al. (2000) to determine
instrumental noise variance worked well in field conditions over a long
period of time.</p><?xmltex \hack{\newpage}?>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusions</title>
      <p>The new instruments based on continuous-wave quantum cascade lasers,
AR-CW-QCL and LGR-CW-QCL, were stable throughout of the campaign in terms of determining the absolute concentrations and obtaining close fluxes.</p>
      <p>The older instruments CS-TDL and AR-P-QCL measured systematically different
fluxes over subperiods of the campaign up to <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>29 and <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>36 %,
respectively, compared to the new instruments based on CW-QCL-s, whereas the
systematic differences did not prevail throughout the campaign. The reasons
for the systematic differences were not identified. We suggest that special
emphasis should be on the instrumental stability and correcting procedures
that can systematically affect the accuracy of measured fluxes when
conducting long-term measurements of prevailingly low fluxes.</p>
      <p>The lowest noise level was determined for AR-CW-QCL (0.12 ppb at 10 Hz
sampling rate) and the highest for the old-generation instrument CS-TDL
(precision 2 ppb at 10 Hz sampling rate). During the period DOY 206–272,
when all instruments were operational, the lower-quantile/median/upper-quantile statistics of the fluxes measured by AR-CW-QCL instrument were
0.008/0.11/0.31 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, respectively.</p>
      <p>The random errors of fluxes originate from the stochastic nature of
turbulence (one-point sampling over limited time interval). Additionally, the
instrumental noise contributes to the random flux error. The median values
for flux errors during the period DOY 206–272 (error due to instrumental
noise/total error) were detected for the instruments as follows: for
CS-TDL 0.155/0.255, AR-CW-QCL 0.010/0.036, LGR-CW-QCL 0.046/0.065 and
AR-P-QCL 0.031/0.068 nmol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. These error statistics
indicate that (i) the major component of the flux random error source is the
instrumental noise and (ii) the flux errors for CS-TDL are dominantly larger
than the flux magnitude, and only in the case of AR-CW-QCL can the flux error due to
instrumental noise be said to be much smaller than the typical flux
value.</p>
      <p>The following fractions of fluxes were smaller than the stochastic flux
error: in the case of CS-TDL, 47 %; AR-CW-QCL, 15 %; LGR-CW-QCL,
28 %; and AR-P-QCL, 30 %. We conclude that apart from AR-CW-QCL, a large fraction
of the fluxes were within the error magnitude of single half-hour
observations.</p>
      <p>With the new-generation analysers based on continuous-wave QCL-s, N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O
fluxes can be measured with the EC at locations where the fluxes are small,
well below the detection limit of older instruments (CS-TDL for instance).
According to our analysis, the new instruments enable one to attain the flux
precision as good as the precision of the modern chamber systems. Thus, the
new instruments open up the possibility of studying N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O exchange in new
ecosystems, broadening scientific perspectives.</p><?xmltex \hack{\newpage}?>
</sec>

      
      </body>
    <back><ack><title>Acknowledgements</title><p>This work was supported by the Academy of Finland (project nos. 118780 and
127456). ICOS (271878), ICOS-Finland (281255) and ICOS-ERIC (281250), DEFROST
Nordic Centre of Excellence and InGOS EU are gratefully acknowledged for
funding this work. This work was also supported by institutional research
funding (IUT20-11) of the Estonian Ministry of Education and Research. The
UEF part of the research work was supported by the funding from the UEF
infrastructure funding, Academy of Finland FidiPro programme (PIs – Profs
Pertti Martikainen and Seppo Kellomäki) and the Ministry of Agriculture
and Forestry, Finland. <?xmltex \hack{\newline}?><?xmltex \hack{\newline}?> Edited by: A. Neftel</p></ack><ref-list>
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