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compiling for Linux

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Roland Hollós 2019-12-02 14:07:45 +01:00
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commit 89d362f27d
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119
RBBGCMuso/inst/examples/hhs/CO2.txt Normal file
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1900 296.10
1901 296.10
1902 296.50
1903 296.80
1904 297.20
1905 297.60
1906 298.10
1907 298.50
1908 298.90
1909 299.30
1910 299.70
1911 300.10
1912 300.40
1913 300.80
1914 301.10
1915 301.40
1916 301.70
1917 302.10
1918 302.40
1919 302.70
1920 303.00
1921 303.40
1922 303.80
1923 304.10
1924 304.50
1925 305.00
1926 305.40
1927 305.80
1928 306.30
1929 306.80
1930 307.20
1931 307.70
1932 308.20
1933 308.60
1934 309.00
1935 309.40
1936 309.80
1937 310.00
1938 310.20
1939 310.30
1940 310.40
1941 310.40
1942 310.30
1943 310.20
1944 310.10
1945 310.10
1946 310.10
1947 310.20
1948 310.30
1949 310.50
1950 310.70
1951 311.10
1952 311.50
1953 311.90
1954 312.40
1955 313.00
1956 313.60
1957 314.20
1958 314.90
1959 315.79
1960 316.61
1961 317.33
1962 318.08
1963 318.70
1964 319.36
1965 320.02
1966 321.09
1967 321.99
1968 322.93
1969 324.21
1970 325.24
1971 326.06
1972 327.18
1973 328.84
1974 329.73
1975 330.73
1976 331.83
1977 333.25
1978 334.60
1979 336.85
1980 338.69
1981 339.93
1982 341.13
1983 342.78
1984 344.42
1985 345.90
1986 347.15
1987 348.93
1988 351.48
1989 352.91
1990 354.19
1991 355.59
1992 356.37
1993 357.04
1994 358.88
1995 360.88
1996 362.64
1997 363.76
1998 366.63
1999 368.31
2000 369.48
2001 372.59
2002 374.37
2003 378.04
2004 380.88
2005 383.88
2006 385.64
2007 385.76
2008 386.13
2009 387.37
2010 389.85
2011 391.62
2012 393.82
2013 396.48
2014 398.61
2015 400.00
2016 401.00
2017 402.00
2018 404.00

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1900 0.0003911
1901 0.0003922
1902 0.0003952
1903 0.0003982
1904 0.0004012
1905 0.0004043
1906 0.0004073
1907 0.0004103
1908 0.0004133
1909 0.0004164
1910 0.0004224
1911 0.0004267
1912 0.0004310
1913 0.0004353
1914 0.0004396
1915 0.0004439
1916 0.0004482
1917 0.0004525
1918 0.0004568
1919 0.0004611
1920 0.0004697
1921 0.0004741
1922 0.0004786
1923 0.0004830
1924 0.0004875
1925 0.0004919
1926 0.0004964
1927 0.0005008
1928 0.0005053
1929 0.0005097
1930 0.0005186
1931 0.0005214
1932 0.0005243
1933 0.0005271
1934 0.0005299
1935 0.0005327
1936 0.0005356
1937 0.0005384
1938 0.0005412
1939 0.0005440
1940 0.0005497
1941 0.0005600
1942 0.0005703
1943 0.0005806
1944 0.0005909
1945 0.0006013
1946 0.0006116
1947 0.0006219
1948 0.0006322
1949 0.0006425
1950 0.0006632
1951 0.0006775
1952 0.0006919
1953 0.0007063
1954 0.0007207
1955 0.0007350
1956 0.0007494
1957 0.0007638
1958 0.0007782
1959 0.0007925
1960 0.0008213
1961 0.0008407
1962 0.0008601
1963 0.0008795
1964 0.0008989
1965 0.0009183
1966 0.0009378
1967 0.0009572
1968 0.0009766
1969 0.0009960
1970 0.0010348
1971 0.0010591
1972 0.0010465
1973 0.0010524
1974 0.0010582
1975 0.0010641
1976 0.0010699
1977 0.0010758
1978 0.0010816
1979 0.0010875
1980 0.0010933
1981 0.0010992
1982 0.0011050
1983 0.0011109
1984 0.0011167
1985 0.0011226
1986 0.0011284
1987 0.0011343
1988 0.0011401
1989 0.0011460
1990 0.0011519
1991 0.0011577
1992 0.0011636
1993 0.0011694
1994 0.0011753
1995 0.0011811
1996 0.0011870
1997 0.0011928
1998 0.0011987
1999 0.0012045
2000 0.0012104
2001 0.0012239
2002 0.0012347
2003 0.0012654
2004 0.0012762
2005 0.0012870
2006 0.0012977
2007 0.0013085
2008 0.0013192
2009 0.0013200
2010 0.0013407
2011 0.0013515
2012 0.0013722
2013 0.0013830
2014 0.0013938
2015 0.0014010
2016 0.0014020
2017 0.0014040
2018 0.0014050

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ECOPHYS FILE - C3 grass muso6
----------------------------------------------------------------------------------------
FLAGS
0 (flag) biome type flag (1 = WOODY 0 = NON-WOODY)
0 (flag) woody type flag (1 = EVERGREEN 0 = DECIDUOUS)
1 (flag) photosyn. type flag (1 = C3 PSN 0 = C4 PSN)
----------------------------------------------------------------------------------------
PLANT FUNCTIONING PARAMETERS
0 (yday) yearday to start new growth (when phenology flag = 0)
364 (yday) yearday to end litterfall (when phenology flag = 0)
1.0 (prop.) transfer growth period as fraction of growing season (when transferGDD_flag = 0)
1.0 (prop.) litterfall as fraction of growing season (when transferGDD_flag = 0)
0 (Celsius) base temperature
-9999 (Celsius) minimum temperature for growth displayed on current day (-9999: no T-dependence)
-9999 (Celsius) optimal1 temperature for growth displayed on current day (-9999: no T-dependence)
-9999 (Celsius) optimal2 temperature for growth displayed on current day (-9999: no T-dependence)
-9999 (Celsius) maxmimum temperature for growth displayed on current day (-9999: no T-dependence)
-9999 (Celsius) minimum temperature for carbon assimilation on current day (-9999: no T-dependence)
-9999 (Celsius) optimal1 temperature for carbon assimilation on current day (-9999: no T-dependence)
-9999 (Celsius) optimal2 temperature for carbon assimilation on current day (-9999: no T-dependence)
-9999 (Celsius) maxmimum temperature for carbon assimilation on current day (-9999: no T-dependence)
1.0 (1/yr) annual leaf and fine root turnover fraction
0.00 (1/yr) annual live wood turnover fraction
0.0 (1/yr) annual fire mortality fraction
0.01 (1/vegper) whole-plant mortality fraction in vegetation period
36.6 (kgC/kgN) C:N of leaves
45.0 (kgC/kgN) C:N of leaf litter, after retranslocation
50.0 (kgC/kgN) C:N of fine roots
36.6 *(kgC/kgN) C:N of fruit
36.6 (kgC/kgN) C:N of soft stem
0.0 *(kgC/kgN) C:N of live wood
0.0 *(kgC/kgN) C:N of dead wood
0.4 (kgC/kgDM) dry matter carbon content of leaves
0.4 (kgC/kgDM) dry matter carbon content of leaf litter
0.4 (kgC/kgDM) dry matter carbon content of fine roots
0.4 *(kgC/kgDM) dry matter carbon content of fruit
0.4 (kgC/kgDM) dry matter carbon content of soft stem
0.4 *(kgC/kgDM) dry matter carbon content of live wood
0.4 *(kgC/kgDM) dry matter carbon content of dead wood
0.68 (DIM) leaf litter labile proportion
0.23 (DIM) leaf litter cellulose proportion
0.34 (DIM) fine root labile proportion
0.44 (DIM) fine root cellulose proportion
0.68 *(DIM) fruit litter labile proportion
0.23 *(DIM) fruit litter cellulose proportion
0.68 (DIM) soft stem litter labile proportion
0.23 (DIM) soft stem litter cellulose proportion
0.00 *(DIM) dead wood cellulose proportion
0.01 (1/LAI/d) canopy water interception coefficient
0.7 (DIM) canopy light extinction coefficient
0.6 (g/MJ) potential radiation use efficiency
0.781 (DIM) radiation parameter1 (Jiang et al.2015)
-13.596 (DIM) radiation parameter2 (Jiang et al.2015)
2.0 (DIM) all-sided to projected leaf area ratio
2.0 (DIM) ratio of shaded SLA:sunlit SLA
0.3 (DIM) fraction of leaf N in Rubisco
0.03 (DIM) fraction of leaf N in PEP Carboxylase
0.002 (m/s) maximum stomatal conductance (projected area basis)
0.00006 (m/s) cuticular conductance (projected area basis)
0.039 (m/s) boundary layer conductance (projected area basis)
1.0 (m) maximum height of plant
0.8 (kgC) stem weight corresponding to maximum height
0.5 (dimless) plant height function shape parameter (slope)
1.0 (m) maximum depth of rooting zone
2.67 (DIM) root distribution parameter
0.4 (kgC) root weight corresponding to max root depth
0.5 (dimless) root depth function shape parameter (slope)
1000 (m/kg) root weight to rooth length conversion factor
0.3 (prop.) growth resp per unit of C grown
0.195 (kgC/kgN/d) maintenance respiration in kgC/day per kg of tissue N
0.1 (DIM) theoretical maximum prop. of non-structural and structural carbohydrates
0.24 (DIM) prop. of non-structural carbohydrates available for maintanance respiration
0.0048 (kgN/m2/yr) symbiotic+asymbiotic fixation of N
0 (day) time delay for temperature in photosynthesis acclimation
----------------------------------------------------------------------------------------
CROP SPECIFIC PARAMETERS
1 (DIM) number of phenophase of germination (from 1 to 7; 0: NO specific)
2 (DIM) number of phenophase of emergence (from 1 to 7; 0: NO specific)
0.5 (prop.) critical VWCratio (prop. to FC-WP) in germination
0 (DIM) number of phenophase of photoperiodic slowing effect (from 1 to 7; 0: NO effect)
20 (hour) critical photoslow daylength
0.005 (DIM) slope of relative photoslow development rate
0 (DIM) number of phenophase of vernalization (from 1 to 7; 0: NO effect)
0 (Celsius) critical vernalization temperature 1
5 (Celsius) critical vernalization temperature 2
8 (Celsius) critical vernalization temperature 3
15 (Celsius) critical vernalization temperature 4
0.04 (DIM) slope of relative vernalization development rate
50 (n) required vernalization days (in vernalization development rate)
0 (DIM) number of flowering phenophase (from 1 to 7;0: NO effect)
35 (Celsius) critical flowering heat stress temperature 1
40 (Celsius) critical flowering heat stress temperature 2
0.2 (prop.) theoretical maximum of flowering thermal stress mortality parameter
----------------------------------------------------------------------------------------
STRESS AND SENESCENCE PARAMETERS
1.0 (prop) VWC ratio to calc. soil moisture limit 1 (prop. to FC-WP)
0.95 (prop) VWC ratio to calc. soil moisture limit 2 (prop. to SAT-FC)
0.4 (prop) minimum of soil moisture limit2 multiplicator (full anoxic stress value)
1000 (Pa) vapor pressure deficit: start of conductance reduction
2800 (Pa) vapor pressure deficit: complete conductance reduction
0.03 (prop.) maximum senescence mortality coefficient of aboveground plant material
0.02 (prop.) maximum senescence mortality coefficient of belowground plant material
0.01 (prop.) maximum senescence mortality coefficient of non-structured plant material
35 (Celsius) lower limit extreme high temperature effect on senescence mortality
40 (Celsius) upper limit extreme high temperature effect on senescence mortality
0.01 (prop.) turnover rate of wilted standing biomass to litter
0.047 (prop.) turnover rate of non-woody cut-down biomass to litter
0.01 (prop.) turnover rate of woody cut-down biomass to litter
30 (nday) drought tolerance parameter (critical value of DSWS)
----------------------------------------------------------------------------------------
GROWING SEASON PARAMETERS
5 (kg/m2) crit. amount of snow limiting photosyn.
20 (Celsius) limit1 (under:full constrained) of HEATSUM index
60 (Celsius) limit2 (above:unconstrained) of HEATSUM index
0 (Celsius) limit1 (under:full constrained) of TMIN index
5 (Celsius) limit2 (above:unconstrained) of TMIN index
4000 (Pa) limit1 (above:full constrained) of VPD index
1000 (Pa) limit2 (under:unconstrained) of VPD index
0 (s) limit1 (under:full constrained) of DAYLENGTH index
0 (s) limit2 (above:unconstrained) of DAYLENGTH index
10 (day) moving average (to avoid the effects of extreme events)
0.10 (dimless) GSI limit1 (greater that limit -> start of vegper)
0.01 (dimless) GSI limit2 (less that limit -> end of vegper)
----------------------------------------------------------------------------------------
PHENOLOGICAL (ALLOCATION) PARAMETERS (7 phenological phases)
phase1 phase2 phase3 phase4 phase5 phase6 phase7 (text) name of the phenophase
10 200 500 200 400 200 100 (Celsius) length of phenophase (GDD)
0.3 0.3 0.3 0.3 0.3 0.3 0.3 (ratio) leaf ALLOCATION
0.52 0.52 0.52 0.52 0.52 0.52 0.52 (ratio) fine root ALLOCATION
0.0 0.0 0.0 0.0 0.0 0.0 0.0 (ratio) fruit ALLOCATION
0.18 0.18 0.18 0.18 0.18 0.18 0.18 (ratio) soft stem ALLOCATION
0 0 0 0 0 0 0 (ratio) live woody stem ALLOCATION
0 0 0 0 0 0 0 (ratio) dead woody stem ALLOCATION
0 0 0 0 0 0 0 (ratio) live coarse root ALLOCATION
0 0 0 0 0 0 0 (ratio) dead coarse root ALLOCATION
49 49 49 49 49 49 49 (m2/kgC) canopy average specific leaf area (projected area basis)
0.37 0.37 0.37 0.37 0.37 0.37 0.37 (prop.) current growth proportion
10000 10000 10000 10000 10000 10000 10000 (Celsius) maximal lifetime of plant tissue

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System: Linux meteor30 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) x86_64 GNU/Linux
Compilation time: Mon 02 Dec 2019 02:03:10 PM CET
Compiler: gcc (Debian 8.3.0-6) 8.3.0
Compiler flags:
Model version: 6.0.3

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MANAGEMENT_INFORMATION MuSo6
-------------------------------------------------------------------------------------------------------------------
PLANTING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none
-------------------------------------------------------------------------------------------------------------------
THINNING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none
-------------------------------------------------------------------------------------------------------------------
MOWING
1 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
hhs.mow
-------------------------------------------------------------------------------------------------------------------
GRAZING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none
-------------------------------------------------------------------------------------------------------------------
HARVESTING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none
-------------------------------------------------------------------------------------------------------------------
PLOUGHING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none
-------------------------------------------------------------------------------------------------------------------
FERTILIZING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none
-------------------------------------------------------------------------------------------------------------------
IRRIGATING
0 (flag) flag of management action: 0 - no MGM, 1 - MGM information from file below
none

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DATE afterLAI(m2/m2) transPART(%)
2007.06.06 0.5 90
2007.08.20 0.4 80
2008.06.06 0.5 90
2008.08.20 0.4 80
2009.06.06 0.5 90
2009.08.20 0.4 80
2010.06.06 0.5 90
2010.08.20 0.4 80
2011.06.06 0.5 90
2011.08.20 0.4 80
2012.06.06 0.5 90
2012.08.20 0.4 80
2013.06.06 0.5 90
2013.08.20 0.4 80
2014.06.06 0.5 90
2014.08.20 0.4 80
2015.06.06 0.5 90
2015.08.20 0.4 80

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SOILPROP FILE - hhs muso6
----------------------------------------------------------------------------------------
NITROGEN AND DECOMPOSITION PARAMETERS
0.02 (prop.) denitrification rate per g of CO2 respiration of SOM
0.2 (prop.) nitrification coefficient 1
0.07 (prop.) nitrification coefficient 2
0.02 (prop.) coefficient of N2O emission of nitrification
0.1 (prop.) NH4 mobilen proportion
1.0 (prop.) NO3 mobilen proportion
10 (m) e-folding depth of decomposition rate's depth scalar
0.002 (prop.) fraction of dissolved part of SOIL1 organic matter
0.002 (prop.) fraction of dissolved part of SOIL2 organic matter
0.002 (prop.) fraction of dissolved part of SOIL3 organic matter
0.002 (prop.) fraction of dissolved part of SOIL4 organic matter
----------------------------------------------------------------------------------------
RATE SCALARS
0.35 (prop) respiration fractions for fluxes between compartments (l1s1)
0.50 (prop) respiration fractions for fluxes between compartments (l2s2)
0.26 (prop) respiration fractions for fluxes between compartments (l4s3)
0.25 (prop) respiration fractions for fluxes between compartments (s1s2)
0.41 (prop) respiration fractions for fluxes between compartments (s2s3)
0.50 (prop) respiration fractions for fluxes between compartments (s3s4)
0.7 (1/day) rate constant scalar of labile litter pool
0.07 (1/day) rate constant scalar of cellulose litter pool
0.014 (1/day) rate constant scalar of lignin litter pool
0.07 (1/day) rate constant scalar of fast microbial recycling pool
0.014 (1/day) rate constant scalar of medium microbial recycling pool
0.0014 (1/day) rate constant scalar of slow microbial recycling pool
0.0001 (1/day) rate constant scalar of recalcitrant SOM (humus) pool
0.001 (1/day) rate constant scalar of physical fragmentation of coarse woody debris
----------------------------------------------------------------------------------------
CH4 PARAMETERS
212.5 (DIM) soil CH4 emission bulk density dependence parameter1
1.81 (DIM) soil CH4 emission bulk density dependence parameter2
-1.353 (DIM) soil CH4 emission soil water content dependence parameter1
0.2 (DIM) soil CH4 emission soil water content dependence parameter2
1.781 (DIM) soil CH4 emission soil water content dependence parameter3
6.786 (DIM) soil CH4 emission soil water content dependence parameter4
0.010 (DIM) soil CH4 emission soil temperature dependence parameter1
----------------------------------------------------------------------------------------
SOIL PARAMETERS
2 (m) depth of soil
6 (mm) limit of first stage evaporation
20.00 (mm) maximum height of pond water
-9999 (dimless) measured runoff curve number (-9999: no measured data, model estimation)
----------------------------------------------------------------------------------------
SOIL COMPOSITION AND CHARACTERISTIC VALUES (-9999: no measured data)
30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 (%) sand percentage by volume in rock-free soil
50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 (%) silt percentage by volume in rock-free soil
7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 (dimless) soil pH (dimless) measured runoff curve number
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (g/cm3) bulk density
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at saturation
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at field capacity
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at wilting point
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at hygroscopic water content
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (dimless) drainage coefficient
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (cm/day) hydraulic condictivity at saturation

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