LandscapeDNDC  1.36.0
Public Member Functions | Private Member Functions | Static Private Attributes | List of all members
ldndc::SoilChemistryMeTrX Class Reference

Biogeochemical model MeTrx. More...

Inherits ldndc::MBE_LegacyModel.

Public Member Functions

lerr_t solve ()
 

Private Member Functions

lerr_t MeTrX_write_output ()
 
lerr_t MeTrX_write_output_daily ()
 
lerr_t MeTrX_write_output_yearly ()
 
lerr_t MeTrX_write_output_layer_daily ()
 
lerr_t MeTrX_write_output_layer_yearly ()
 
lerr_t MeTrX_write_output_fluxes ()
 
lerr_t MeTrX_write_output_pools ()
 
lerr_t MeTrX_write_output_subdaily ()
 
lerr_t MeTrX_write_rates ()
 
lerr_t MeTrX_fertilize ()
 
lerr_t MeTrX_manure ()
 
lerr_t MeTrX_till ()
 
lerr_t MeTrX_reset ()
 
lerr_t MeTrX_reset_subdaily ()
 
lerr_t MeTrX_reset_daily ()
 
lerr_t MeTrX_update ()
 
lerr_t MeTrX_check_for_negative_value (char const *)
 iterates over complete soilchemistry state and checks for negative values
 
lerr_t MeTrX_spinup ()
 
lerr_t MeTrX_physics ()
 
void MeTrX_leaching ()
 Downwards transport of solutes, litter and humus with percolation water. More...
 
void MeTrX_groundwater_access ()
 
lerr_t MeTrX_plant_respiration (size_t)
 Updates o2 and co2 concentrations in soil layers. There is no o2 mass conservation guaranteed because vegetation modules calculate autotrophic respiration without oxygen limitation. When oxygen demand in soil layers is not fullfilled o2_deff stores deficit and increases oxygen demand in following layers.
 
lerr_t MeTrX_freeze_thaw ()
 
lerr_t MeTrX_fragmentation ()
 
void MeTrX_litter_distribution (double const &, double const &, double const &, double const &, double const &, double const &, CBM_Vector< double > &accumulated_litter_sl)
 Adds carbon and nitrogen litter to soil litter pools.
 
lerr_t MeTrX_gas_diffusion ()
 
void MeTrX_liq_diffusion ()
 
lerr_t MeTrX_pertubation ()
 
lerr_t MeTrX_metabolism ()
 
lerr_t MeTrX_dissolution ()
 
void MeTrX_ebullition ()
 
void MeTrX_iron_reduction ()
 
void MeTrX_iron_oxidation ()
 
void MeTrX_algae_dynamics ()
 
void MeTrX_ch4_production ()
 
void MeTrX_ch4_oxidation ()
 
void MeTrX_microbial_dynamics ()
 
void MeTrX_soil_organic_matter_turnover ()
 
lerr_t MeTrX_fermentation ()
 
void MeTrX_urea_hydrolysis ()
 
void MeTrX_pH_calculation ()
 
lerr_t MeTrX_nitrogen_fertilizer_release ()
 Transforms nitrogen from slow release nitrogen fertilizer to nh4. More...
 
void MeTrX_nitrification ()
 
void MeTrX_denitrification ()
 
void MeTrX_chemodenitrification ()
 
void MeTrX_clay_nh4_equilibrium ()
 
void MeTrX_nh3_nh4_equilibrium ()
 
void MeTrX_anaerobic_volume ()
 
double MeTrX_get_ph_sl (size_t)
 Returns dynamic pH-value of given soil layer.
 
double MeTrX_get_ph_wl ()
 
double MeTrX_get_fact_tm_decomp (size_t const &)
 Response function for decomposition of organic matter depeding on temperature and moisture. More...
 
double MeTrX_get_fact_tm_denit (size_t const &)
 Response function for denitrification depending on temperature and moisture.
 
double MeTrX_get_k_mm_x_sl (size_t const &_sl, double const &_k_mm)
 Scales Michaelis-Menten constant according to spatial discretization.
 
double MeTrX_get_c_tot ()
 
double MeTrX_get_n_tot ()
 
lerr_t MeTrX_receive_state ()
 
lerr_t MeTrX_send_state ()
 
lerr_t MeTrX_dissolution_soil (double const &, double &, double &)
 
lerr_t MeTrX_update_soil_discretization ()
 

Static Private Attributes

static const double TNORM = 293.2
 
static const double N_MINERALISATION_FRACTION = 0.5
 

Detailed Description

Biogeochemical model MeTrx.

Member Function Documentation

◆ MeTrX_algae_dynamics()

void ldndc::SoilChemistryMeTrX::MeTrX_algae_dynamics ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_anaerobic_volume()

void ldndc::SoilChemistryMeTrX::MeTrX_anaerobic_volume ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by MeTrX_pertubation(), and solve().

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◆ MeTrX_ch4_oxidation()

void ldndc::SoilChemistryMeTrX::MeTrX_ch4_oxidation ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_ch4_production()

void ldndc::SoilChemistryMeTrX::MeTrX_ch4_production ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_chemodenitrification()

void ldndc::SoilChemistryMeTrX::MeTrX_chemodenitrification ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by MeTrX_get_fact_tm_denit(), and solve().

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◆ MeTrX_clay_nh4_equilibrium()

void ldndc::SoilChemistryMeTrX::MeTrX_clay_nh4_equilibrium ( )
private
Parameters
[in]None
[out]None
Returns
void

References ldndc::cation_exchange_capacity().

Referenced by solve().

95 {
96  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
97  {
98  /* partitioning coefficient */
99  double const k_nh4( 1.0);
100 
101  /* total mount of n-nh4 [1e3:g] */
102  double const nh4_sol_old( nh4_ae_sl[sl] + nh4_an_sl[sl]);
103  double const nh4_total( nh4_sol_old + sc_.clay_nh4_sl[sl]);
104 
105  /* soil mass [1e3:g] */
106  double const m_soil( sc_.get_soil_mass( sl));
107 
108  /* soil organic matter content [%] */
109  double const som_percentage( sc_.som_sl[sl] / m_soil * 100.0);
110 
111  /* cation exchange capacity [1e-2:mol] */
112  double const cec( cation_exchange_capacity(
113  sc_.clay_sl[sl] * 100.0,
114  sc_.sand_sl[sl] * 100.0,
115  som_percentage,
116  sc_.ph_sl[sl],
117  ECOSYS_GRASSLAND) * m_soil);
118 
119  /* n-h4 exchange capacity [kg] */
120  double const nh4_capacity( cec * cbm::MN * 1.0e-5);
121 
122  /* nh4 per soil mass [1e-5:mol:g] */
123  double const nh4_total_percentage( nh4_total * 1.0e5 / (cbm::MN * m_soil));
124 
125  /* adsorbed nh4 percentage [%] */
126  double const nh4_clay_percentage( k_nh4 * nh4_total_percentage);
127 
128  /* adsorbed nh4 */
129  double const nh4_clay( cbm::bound_max( nh4_clay_percentage * 1.0e-2 * nh4_capacity, nh4_total));
130 
131  /* nh4 - clay_nh4 exchange */
132  double const delta_nh4( (nh4_clay - sc_.clay_nh4_sl[sl]) * FTS_TOT_);
133 
134  sc_.clay_nh4_sl[sl] += delta_nh4;
135  double const nh4_sol_new( nh4_total - sc_.clay_nh4_sl[sl]);
136  if ( cbm::flt_greater_zero( nh4_sol_old))
137  {
138  nh4_ae_sl[sl] = nh4_ae_sl[sl] / nh4_sol_old * nh4_sol_new;
139  nh4_an_sl[sl] = nh4_sol_new - nh4_ae_sl[sl];
140  }
141  else
142  {
143  nh4_ae_sl[sl] = nh4_sol_new * (1.0 - sc_.anvf_sl[sl]);
144  nh4_an_sl[sl] = nh4_sol_new * sc_.anvf_sl[sl];
145  }
146  }
147 }
ldndc::cation_exchange_capacity
double LDNDC_API cation_exchange_capacity(double _clay, double _sand, double _som, double _ph, ecosystem_type_e _ecosystem)
Detailed description provided here .
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◆ MeTrX_denitrification()

void ldndc::SoilChemistryMeTrX::MeTrX_denitrification ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_dissolution()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_dissolution ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_groundwater_access(), and solve().

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◆ MeTrX_dissolution_soil()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_dissolution_soil ( double const &  _henry,
double &  _val_gas,
double &  _val_liq 
)
private
Parameters
[in]_henryNone
[in,out]_gasgaseous species
[in,out]_liqdissolved substance
Returns
error code

Referenced by MeTrX_groundwater_access().

521 {
522  double const val_tot( _val_gas + _val_liq);
523  if ( cbm::flt_greater_zero( val_tot))
524  {
525  _val_liq = _henry / (1.0 + _henry) * val_tot;
526  _val_gas = val_tot - _val_liq;
527  }
528  return LDNDC_ERR_OK;
529 }
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◆ MeTrX_ebullition()

void ldndc::SoilChemistryMeTrX::MeTrX_ebullition ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by MeTrX_groundwater_access(), and solve().

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◆ MeTrX_fermentation()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_fermentation ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by solve().

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◆ MeTrX_fertilize()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_fertilize ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by solve().

33 {
34  EventAttributes const * ev_fert = NULL;
35  while (( ev_fert = this->m_FertilizeEvents.pop()) != NULL)
36  {
37  double new_fertilizer_n( -sc_.accumulated_n_fertilizer);
38  //
39  cbm::string_t const fertilizer = ev_fert->get( "/type", "?");
40  //
41  double const f_depth = ev_fert->get( "/depth", 0.0);
42 
43  // amount of fertilizer [kg:ha-1]
44  double const n_amount( ev_fert->get( "/amount", 0.0));
45 
46  // amount of nitrification inhibitor [kg:ha-1]
47  double const ni_amount( ev_fert->get( "/ni_amount", 0.0));
48 
49  // amount of urease inhibitor [kg:ha-1]
50  double const ui_amount( ev_fert->get( "/ui_amount", 0.0));
51 
52  if ( have_water_table &&
53  cbm::flt_equal_zero( f_depth))
54  {
55  double const n_amount_sbl( n_amount / (cbm::M2_IN_HA * sb_.surfacebulk_layer_cnt()));
56  double const ni_amount_sbl( ni_amount / (cbm::M2_IN_HA * sb_.surfacebulk_layer_cnt()));
57  double const ui_amount_sbl( ui_amount / (cbm::M2_IN_HA * sb_.surfacebulk_layer_cnt()));
58 
59  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
60  {
61  if ( fertilizer == "nh4no3" )
62  {
63  sb_.nh4_sbl[sbl] += 0.5 * n_amount_sbl;
64  sb_.no3_sbl[sbl] += 0.5 * n_amount_sbl;
65  accumulated_n_nh4_fertilization_sbl[sbl] += 0.5 * n_amount_sbl;
66  accumulated_n_no3_fertilization_sbl[sbl] += 0.5 * n_amount_sbl;
67  sc_.accumulated_n_fertilizer += n_amount_sbl;
68  }
69  else if ( fertilizer == "nh3" )
70  {
71  sb_.nh3_sbl[sbl] += n_amount_sbl;
72  accumulated_n_nh3_fertilization_sbl[sbl] += n_amount_sbl;
73  sc_.accumulated_n_fertilizer += n_amount_sbl;
74  }
75  else if ( fertilizer == "no3" )
76  {
77  sb_.no3_sbl[sbl] += n_amount_sbl;
78  accumulated_n_no3_fertilization_sbl[sbl] += n_amount_sbl;
79  sc_.accumulated_n_fertilizer += n_amount_sbl;
80  }
81  else if (( fertilizer == "nh4" ) || ( fertilizer == "nh4hco3" ) || ( fertilizer == "nh4hpo4" ))
82  {
83  sb_.nh4_sbl[sbl] += n_amount_sbl;
84  accumulated_n_nh4_fertilization_sbl[sbl] += n_amount_sbl;
85  sc_.accumulated_n_fertilizer += n_amount_sbl;
86  }
87  else if ( fertilizer == "nh4so4" )
88  {
89  sb_.so4_sbl[sbl] += n_amount_sbl * (cbm::MS / cbm::MN);
90  sb_.nh4_sbl[sbl] += n_amount_sbl;
91  accumulated_n_nh4_fertilization_sbl[sbl] += n_amount_sbl;
92  sc_.accumulated_n_fertilizer += n_amount_sbl;
93  }
94  else if ( fertilizer == "so4" )
95  {
96  sb_.so4_sbl[sbl] += n_amount_sbl;
97  }
98  else if ( fertilizer == "urea" )
99  {
100  sb_.urea_sbl[sbl] += n_amount_sbl;
101  accumulated_n_urea_fertilization_sbl[sbl] += n_amount_sbl;
102  sc_.accumulated_n_fertilizer += n_amount_sbl;
103  }
104  /* controled release nitrogen fertilizer */
105  else if ( fertilizer == "crnf" )
106  {
107  crnf_.add_crnf( n_amount_sbl);
108  sb_.coated_nh4_sbl[sbl] += n_amount_sbl;
109  sc_.accumulated_n_fertilizer += n_amount_sbl;
110  }
111  else
112  {
113  KLOGWARN( "Unknown fertilizer type \"",fertilizer,"\". Ignoring event!");
114  }
115 
116  sb_.ni_sbl[sbl] += ni_amount_sbl;
117  sb_.ui_sbl[sbl] += ui_amount_sbl;
118  crnf_.add_nitrification_inhibitior( ni_amount_sbl);
119  }
120  }
121  else
122  {
123  size_t l_0( 0);
124  size_t l_1( 1);
125  if ( cbm::flt_equal_zero( f_depth))
126  {
127  l_0 = 0;
128  l_1 = 1;
129  for( size_t sl = 1; sl < sl_.soil_layer_cnt(); ++sl)
130  {
131  if ( sc_.depth_sl[sl] <= 0.01)
132  {
133  l_1 = sl;
134  }
135  else{ break; }
136  }
137  }
138  else
139  {
140  //l_0 not allowed to be deeper than last but one soil layer
141  l_0 = sl_.soil_layer_cnt()-2;
142  //find first layer (from top) having at least depth <depth(fert)>
143  for ( size_t l = 0; l < sl_.soil_layer_cnt()-1; ++l)
144  {
145  if ( cbm::flt_greater_equal( sc_.depth_sl[l], f_depth))
146  {
147  l_0 = l;
148  break;
149  }
150  }
151  //l_1 must at least one layer below l_0
152  l_1 = l_0 + 1;
153  for ( size_t l = l_0 + 1; l < sl_.soil_layer_cnt(); ++l)
154  {
155  /* distribute at least among 4cm soil profile */
156  if ( cbm::flt_greater_equal( sc_.depth_sl[l], f_depth + 0.04))
157  {
158  l_1 = l;
159  break;
160  }
161  }
162  }
163 
164  double const n_amount_per_layer = (n_amount / cbm::M2_IN_HA) / (double)( l_1 - l_0);
165  double const ni_amount_per_layer = (ni_amount / cbm::M2_IN_HA) / (double)( l_1 - l_0);
166  double const ui_amount_per_layer = (ui_amount / cbm::M2_IN_HA) / (double)( l_1 - l_0);
167 
168  for ( size_t sl = l_0; sl < l_1; ++sl)
169  {
170  if ( fertilizer == "nh4no3" )
171  {
172  nh4_ae_sl[sl] += 0.5 * n_amount_per_layer * (1.0 - sc_.anvf_sl[sl]);
173  nh4_an_sl[sl] += 0.5 * n_amount_per_layer * sc_.anvf_sl[sl];
174  no3_ae_sl[sl] += 0.5 * n_amount_per_layer * (1.0 - sc_.anvf_sl[sl]);
175  no3_an_sl[sl] += 0.5 * n_amount_per_layer * sc_.anvf_sl[sl];
176  accumulated_n_nh4_fertilization_sl[sl] += 0.5 * n_amount_per_layer;
177  accumulated_n_no3_fertilization_sl[sl] += 0.5 * n_amount_per_layer;
178  sc_.accumulated_n_fertilizer += n_amount_per_layer;
179  }
180  else if ( fertilizer == "nh3" )
181  {
182  sc_.nh3_liq_sl[sl] += n_amount_per_layer;
183  accumulated_n_nh3_fertilization_sl[sl] += n_amount_per_layer;
184  sc_.accumulated_n_fertilizer += n_amount_per_layer;
185  }
186  else if ( fertilizer == "no3" )
187  {
188  no3_ae_sl[sl] += n_amount_per_layer * (1.0 - sc_.anvf_sl[sl]);
189  no3_an_sl[sl] += n_amount_per_layer * sc_.anvf_sl[sl];
190  accumulated_n_no3_fertilization_sl[sl] += n_amount_per_layer;
191  sc_.accumulated_n_fertilizer += n_amount_per_layer;
192  }
193  else if (( fertilizer == "nh4" ) || ( fertilizer == "nh4hco3" ) || ( fertilizer == "nh4hpo4" ))
194  {
195  nh4_ae_sl[sl] += n_amount_per_layer * (1.0 - sc_.anvf_sl[sl]);
196  nh4_an_sl[sl] += n_amount_per_layer * sc_.anvf_sl[sl];
197  accumulated_n_nh4_fertilization_sl[sl] += n_amount_per_layer;
198  sc_.accumulated_n_fertilizer += n_amount_per_layer;
199  }
200  else if ( fertilizer == "nh4so4" )
201  {
202  sc_.so4_sl[sl] += n_amount_per_layer * (cbm::MS / cbm::MN);
203  nh4_ae_sl[sl] += n_amount_per_layer * (1.0 - sc_.anvf_sl[sl]);
204  nh4_an_sl[sl] += n_amount_per_layer * sc_.anvf_sl[sl];
205  accumulated_n_nh4_fertilization_sl[sl] += n_amount_per_layer;
206  sc_.accumulated_n_fertilizer += n_amount_per_layer;
207  }
208  else if ( fertilizer == "so4" )
209  {
210  sc_.so4_sl[sl] += n_amount_per_layer;
211  }
212  else if ( fertilizer == "urea" )
213  {
214  sc_.urea_sl[sl] += n_amount_per_layer;
215  accumulated_n_urea_fertilization_sl[sl] += n_amount_per_layer;
216  sc_.accumulated_n_fertilizer += n_amount_per_layer;
217  }
218  /* controled release nitrogen fertilizer */
219  else if ( fertilizer == "crnf" )
220  {
221  crnf_.add_crnf( n_amount_per_layer);
222  sc_.coated_nh4_sl[sl] += n_amount_per_layer;
223  accumulated_n_nh4_fertilization_sl[sl] += n_amount_per_layer;
224  sc_.accumulated_n_fertilizer += n_amount_per_layer;
225  }
226  else
227  {
228  KLOGWARN( "Unknown fertilizer type \"",fertilizer,"\". Skipping event!");
229  break;
230  }
231 
232  sc_.ni_sl[sl] += ni_amount_per_layer;
233  sc_.ui_sl[sl] += ui_amount_per_layer;
234  crnf_.add_nitrification_inhibitior( ni_amount_per_layer);
235  }
236  }
237 
238  cbm::state_scratch_t * mcom = io_kcomm->get_scratch();
239 
240  new_fertilizer_n += sc_.accumulated_n_fertilizer;
241  double old_fertilizer_n( 0.0);
242  mcom->get( "fertilize:amount", &old_fertilizer_n, 0.0);
243  mcom->set( "fertilize:amount", old_fertilizer_n + (new_fertilizer_n * cbm::M2_IN_HA));
244  }
245 
246  return LDNDC_ERR_OK;
247 }
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◆ MeTrX_fragmentation()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_fragmentation ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_get_fact_tm_decomp(), and MeTrX_litter_distribution().

Referenced by solve().

25 {
26  /***************/
27  /* wood litter */
28  /***************/
29 
30  /* aboveground wood litter */
31  if ( cbm::flt_greater_zero( sc_.c_wood) ||
32  cbm::flt_greater_zero( sc_.n_wood))
33  {
34  double const k_frag_wood_tm( K_FRAG_WOOD * MeTrX_get_fact_tm_decomp( 0));
35  double const frag_c_wood( k_frag_wood_tm * sc_.c_wood);
36  double const frag_n_wood( k_frag_wood_tm * sc_.n_wood);
37 
38  sc_.c_wood -= frag_c_wood;
39  sc_.n_wood -= frag_n_wood;
40 
41  sc_.c_raw_lit_2_above += 0.5 * frag_c_wood;
42  sc_.c_raw_lit_3_above += 0.5 * frag_c_wood;
43 
44  sc_.n_raw_lit_2_above += 0.5 * frag_n_wood;
45  sc_.n_raw_lit_3_above += 0.5 * frag_n_wood;
46 
47  if ( spinup_.spinup_stage( this->lclock()))
48  {
49  spinup_.exit_wood += frag_c_wood;
50  }
51  }
52 
53 
54  /* belowground wood litter */
55  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
56  {
57  if ( cbm::flt_greater_zero( sc_.c_wood_sl[sl]) ||
58  cbm::flt_greater_zero( sc_.n_wood_sl[sl]))
59  {
60  double const frag_c_wood( K_FRAG_WOOD * MeTrX_get_fact_tm_decomp( sl) * sc_.c_wood_sl[sl]);
61  double const frag_n_wood( K_FRAG_WOOD * MeTrX_get_fact_tm_decomp( sl) * sc_.n_wood_sl[sl]);
62 
63  sc_.c_wood_sl[sl] -= frag_c_wood;
64  sc_.n_wood_sl[sl] -= frag_n_wood;
65 
66  sc_.c_raw_lit_2_sl[sl] += 0.5 * frag_c_wood;
67  sc_.c_raw_lit_3_sl[sl] += 0.5 * frag_c_wood;
68 
69  sc_.n_raw_lit_2_sl[sl] += 0.5 * frag_n_wood;
70  sc_.n_raw_lit_3_sl[sl] += 0.5 * frag_n_wood;
71  }
72  }
73 
74 
75  /******************/
76  /* stubble litter */
77  /******************/
78 
79  if ( cbm::flt_greater_zero( sc_.c_stubble_lit1 + sc_.c_stubble_lit2 + sc_.c_stubble_lit3))
80  {
81  double const k_frag_stubble_tm( K_FRAG_STUBBLE * MeTrX_get_fact_tm_decomp( 0));
82  double const c_senescence_lit1( k_frag_stubble_tm * sc_.c_stubble_lit1);
83  double const c_senescence_lit2( k_frag_stubble_tm * sc_.c_stubble_lit2);
84  double const c_senescence_lit3( k_frag_stubble_tm * sc_.c_stubble_lit3);
85 
86  double const n_senescence_lit1( k_frag_stubble_tm * sc_.n_stubble_lit1);
87  double const n_senescence_lit2( k_frag_stubble_tm * sc_.n_stubble_lit2);
88  double const n_senescence_lit3( k_frag_stubble_tm * sc_.n_stubble_lit3);
89 
90  sc_.c_stubble_lit1 -= c_senescence_lit1;
91  sc_.c_stubble_lit2 -= c_senescence_lit2;
92  sc_.c_stubble_lit3 -= c_senescence_lit3;
93 
94  sc_.n_stubble_lit1 -= n_senescence_lit1;
95  sc_.n_stubble_lit2 -= n_senescence_lit2;
96  sc_.n_stubble_lit3 -= n_senescence_lit3;
97 
98  sc_.c_raw_lit_1_above += c_senescence_lit1;
99  sc_.c_raw_lit_2_above += c_senescence_lit2;
100  sc_.c_raw_lit_3_above += c_senescence_lit3;
101 
102  sc_.n_raw_lit_1_above += n_senescence_lit1;
103  sc_.n_raw_lit_2_above += n_senescence_lit2;
104  sc_.n_raw_lit_3_above += n_senescence_lit3;
105  }
106 
107 
108  /**************/
109  /* raw litter */
110  /**************/
111 
112  /* aboveground */
113  if ( cbm::flt_greater_zero( sc_.c_raw_lit_1_above + sc_.c_raw_lit_2_above + sc_.c_raw_lit_3_above))
114  {
115  double const k_frag_raw_litter_tm( K_FRAG_RAW_LITTER * MeTrX_get_fact_tm_decomp( 0));
116  double const c_senescence_lit1( k_frag_raw_litter_tm * sc_.c_raw_lit_1_above);
117  double const c_senescence_lit2( k_frag_raw_litter_tm * sc_.c_raw_lit_2_above);
118  double const c_senescence_lit3( k_frag_raw_litter_tm * sc_.c_raw_lit_3_above);
119 
120  double const n_senescence_lit1( k_frag_raw_litter_tm * sc_.n_raw_lit_1_above);
121  double const n_senescence_lit2( k_frag_raw_litter_tm * sc_.n_raw_lit_2_above);
122  double const n_senescence_lit3( k_frag_raw_litter_tm * sc_.n_raw_lit_3_above);
123 
124  sc_.c_raw_lit_1_above -= c_senescence_lit1;
125  sc_.c_raw_lit_2_above -= c_senescence_lit2;
126  sc_.c_raw_lit_3_above -= c_senescence_lit3;
127 
128  sc_.n_raw_lit_1_above -= n_senescence_lit1;
129  sc_.n_raw_lit_2_above -= n_senescence_lit2;
130  sc_.n_raw_lit_3_above -= n_senescence_lit3;
131 
132  MeTrX_litter_distribution( n_senescence_lit1, n_senescence_lit2, n_senescence_lit3,
133  c_senescence_lit1, c_senescence_lit2, c_senescence_lit3,
134  accumulated_n_aboveground_raw_litter_fragmentation_sl);
135  }
136 
137  /* belowground */
138  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
139  {
140  if ( cbm::flt_greater_zero( sc_.c_raw_lit_1_sl[sl]))
141  {
142  double const fact_decomp( K_FRAG_RAW_LITTER * MeTrX_get_fact_tm_decomp( sl));
143  double const c_decomp_lit1( fact_decomp * sc_.c_raw_lit_1_sl[sl]);
144  double const c_decomp_lit2( fact_decomp * sc_.c_raw_lit_2_sl[sl]);
145  double const c_decomp_lit3( fact_decomp * sc_.c_raw_lit_3_sl[sl]);
146 
147  double const n_decomp_lit1( fact_decomp * sc_.n_raw_lit_1_sl[sl]);
148  double const n_decomp_lit2( fact_decomp * sc_.n_raw_lit_2_sl[sl]);
149  double const n_decomp_lit3( fact_decomp * sc_.n_raw_lit_3_sl[sl]);
150 
151  sc_.c_raw_lit_1_sl[sl] -= c_decomp_lit1;
152  sc_.c_raw_lit_2_sl[sl] -= c_decomp_lit2;
153  sc_.c_raw_lit_3_sl[sl] -= c_decomp_lit3;
154 
155  sc_.n_raw_lit_1_sl[sl] -= n_decomp_lit1;
156  sc_.n_raw_lit_2_sl[sl] -= n_decomp_lit2;
157  sc_.n_raw_lit_3_sl[sl] -= n_decomp_lit3;
158 
159  sc_.C_lit1_sl[sl] += c_decomp_lit1;
160  sc_.C_lit2_sl[sl] += c_decomp_lit2;
161  sc_.C_lit3_sl[sl] += c_decomp_lit3;
162 
163  sc_.N_lit1_sl[sl] += n_decomp_lit1;
164  sc_.N_lit2_sl[sl] += n_decomp_lit2;
165  sc_.N_lit3_sl[sl] += n_decomp_lit3;
166 
167  accumulated_n_belowground_raw_litter_fragmentation_sl[sl] += n_decomp_lit1 + n_decomp_lit2 + n_decomp_lit3;
168  }
169  }
170 
171 
172  /****************/
173  /* algae litter */
174  /****************/
175 
176  if ( cbm::flt_greater_zero( c_dead_algae) ||
177  cbm::flt_greater_zero( n_dead_algae))
178  {
179  double const fact_decomp( K_FRAG_ALGAE * MeTrX_get_fact_tm_decomp( 0));
180  double const c_decomp_algae( fact_decomp * c_dead_algae);
181  double const n_decomp_algae( fact_decomp * n_dead_algae);
182 
183  c_dead_algae -= c_decomp_algae;
184  n_dead_algae -= n_decomp_algae;
185 
186  MeTrX_litter_distribution( 0.25 * n_decomp_algae, 0.7 * n_decomp_algae, 0.05 * n_decomp_algae,
187  0.25 * c_decomp_algae, 0.7 * c_decomp_algae, 0.05 * c_decomp_algae,
188  accumulated_n_litter_from_algae_sl);
189 
190  dC_litter_algae += c_decomp_algae;
191 
192  if ( !cbm::flt_greater_zero( c_dead_algae))
193  {
194  c_dead_algae = 0.0;
195  }
196  if ( !cbm::flt_greater_zero( n_dead_algae))
197  {
198  n_dead_algae = 0.0;
199  }
200  }
201 
202 
203  /******************/
204  /* dung and urine */
205  /******************/
206 
207  if ( cbm::flt_greater_zero( sc_.c_dung) ||
208  cbm::flt_greater_zero( sc_.n_dung) ||
209  cbm::flt_greater_zero( sc_.n_urine))
210  {
211  MeTrX_litter_distribution( 0.25 * sc_.n_dung, 0.7 * sc_.n_dung, 0.05 * sc_.n_dung,
212  0.25 * sc_.c_dung, 0.7 * sc_.c_dung, 0.05 * sc_.c_dung,
213  accumulated_n_litter_from_dung_sl);
214 
215  for( size_t sl = 0; sl <= SL_SURFACE_DISTRIBUTION; ++sl)
216  {
217  sc_.urea_sl[sl] += sc_.n_urine * SL_SURFACE_DISTRIBUTION_INVERSE;
218  accumulated_n_urea_from_dung_sl[sl] += sc_.n_urine * SL_SURFACE_DISTRIBUTION_INVERSE;
219  }
220 
221  sc_.accumulated_c_livestock_grazing += sc_.c_dung;
222  sc_.accumulated_n_livestock_grazing += sc_.n_dung + sc_.n_urine;
223 
224  sc_.c_dung = 0.0;
225  sc_.n_dung = 0.0;
226  sc_.n_urine = 0.0;
227  }
228 
229  return LDNDC_ERR_OK;
230 }
ldndc::SoilChemistryMeTrX::MeTrX_get_fact_tm_decomp
double MeTrX_get_fact_tm_decomp(size_t const &)
Response function for decomposition of organic matter depeding on temperature and moisture...
Definition: soilchemistry-metrx-decomposition.cpp:661
ldndc::SoilChemistryMeTrX::MeTrX_litter_distribution
void MeTrX_litter_distribution(double const &, double const &, double const &, double const &, double const &, double const &, CBM_Vector< double > &accumulated_litter_sl)
Adds carbon and nitrogen litter to soil litter pools.
Definition: soilchemistry-metrx-fragmentation.cpp:238
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◆ MeTrX_freeze_thaw()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_freeze_thaw ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by solve().

391 {
392  if ( have_freeze_thaw)
393  {
394  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
395  {
396  if (false)
397  {
398  if ( cbm::flt_greater_zero( v_ice_sl[sl]) &&
399  cbm::flt_greater( mc_temp_sl[sl], -0.5))
400  {
401  freeze_thaw_fact_sl[sl] = 1.0;
402  }
403  else if (freeze_thaw_fact_sl[sl] > 0.1)
404  {
405  freeze_thaw_fact_sl[sl] -= 0.3 * FTS_TOT_ * freeze_thaw_fact_sl[sl];
406  }
407  else
408  {
409  freeze_thaw_fact_sl[sl] = 0.0;
410  }
411  }
412 
413  if ( cbm::flt_greater_zero( v_ice_sl[sl]) &&
414  cbm::flt_less_equal( mc_temp_sl[sl], 0.0))
415  {
416  cumulative_freezing_degree_days_sl[sl] += std::abs( mc_temp_sl[sl]) * FTS_TOT_;
417  }
418  else if (cbm::flt_equal_zero( v_ice_sl[sl]) &&
419  cbm::flt_greater_zero( mc_temp_sl[sl]))
420  {
421  if ( cumulative_freezing_degree_days_sl[sl] > 10.0)
422  {
423  double c_decomp_aorg( cbm::bound( 0.0, cumulative_freezing_degree_days_sl[sl] / 400.0, 0.99) * sc_.C_aorg_sl[sl]);
424  double n_decomp_aorg( cbm::bound( 0.0, cumulative_freezing_degree_days_sl[sl] / 400.0, 0.99) * sc_.N_aorg_sl[sl]);
425  sc_.C_aorg_sl[sl] -= c_decomp_aorg;
426  sc_.N_aorg_sl[sl] -= n_decomp_aorg;
427 
428  sc_.an_doc_sl[sl] += c_decomp_aorg * sc_.anvf_sl[sl];
429  sc_.doc_sl[sl] += c_decomp_aorg * (1.0 - sc_.anvf_sl[sl]);
430 
431  don_ae_sl[sl] += (1.0 - sipar_.METRX_FRAC_MINERAL()) * n_decomp_aorg * (1.0 - sc_.anvf_sl[sl]);
432  don_an_sl[sl] += (1.0 - sipar_.METRX_FRAC_MINERAL()) * n_decomp_aorg * sc_.anvf_sl[sl];
433 
434  nh4_ae_sl[sl] += sipar_.METRX_FRAC_MINERAL() * n_decomp_aorg * (1.0 - sc_.anvf_sl[sl]);
435  nh4_an_sl[sl] += sipar_.METRX_FRAC_MINERAL() * n_decomp_aorg * sc_.anvf_sl[sl];
436  }
437 
438  cumulative_freezing_degree_days_sl[sl] = 0.0;
439  }
440  }
441  }
442 
443  return LDNDC_ERR_OK;
444 }
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◆ MeTrX_gas_diffusion()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_gas_diffusion ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_groundwater_access(), and solve().

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◆ MeTrX_get_c_tot()

double ldndc::SoilChemistryMeTrX::MeTrX_get_c_tot ( )
private
Parameters
[in]None
[out]None
Returns
Total soil associated carbon

References MeTrX_get_n_tot().

62 {
63  double c_tot( c_algae + c_dead_algae + sc_.c_wood
64  + sc_.c_stubble_lit1 + sc_.c_stubble_lit2 + sc_.c_stubble_lit3
65  + sc_.c_raw_lit_1_above + sc_.c_raw_lit_2_above + sc_.c_raw_lit_3_above);
66 
67  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
68  {
69  c_tot += ( sc_.c_wood_sl[sl]
70  + sc_.doc_sl[sl] + sc_.an_doc_sl[sl] + doc_ice_sl[sl]
71  + ae_acetate_sl[sl] + an_acetate_sl[sl] + acetate_ice_sl[sl]
72  + sc_.C_micro1_sl[sl] + sc_.C_micro2_sl[sl] + sc_.C_micro3_sl[sl]
73  + sc_.C_aorg_sl[sl] + c_microbial_necromass_sl[sl]
74  + c_humus_1_sl[sl] + c_humus_2_sl[sl] + c_humus_3_sl[sl]
75  + sc_.C_lit1_sl[sl] + sc_.C_lit2_sl[sl] + sc_.C_lit3_sl[sl]
76  + sc_.c_raw_lit_1_sl[sl] + sc_.c_raw_lit_2_sl[sl] + sc_.c_raw_lit_3_sl[sl]
77  + ch4_gas_sl[sl] + ch4_liq_sl[sl]
78  + co2_gas_sl[sl] + co2_liq_sl[sl]);
79  }
80 
81  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
82  {
83  c_tot += sb_.ch4_sbl[sbl] + sb_.co2_sbl[sbl] + sb_.doc_sbl[sbl];
84  }
85 
86  return c_tot;
87 }
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◆ MeTrX_get_fact_tm_decomp()

double ldndc::SoilChemistryMeTrX::MeTrX_get_fact_tm_decomp ( size_t const &  _sl)
private

Response function for decomposition of organic matter depeding on temperature and moisture.

Parameters
[in]_slsoil layer
[out]None
Returns
requested factor

Referenced by MeTrX_fragmentation().

662 {
663  double const fact_t( std::exp( -sipar_.METRX_F_DECOMP_T_EXP_1() *
664  pow(1.0 - mc_temp_sl[_sl] / sipar_.METRX_F_DECOMP_T_EXP_2(), 2.0)));
665  double const fact_m( ldndc::meteo::F_weibull( MeTrX_get_wfps_eff( _sl, 0.0),
666  sipar_.METRX_F_DECOMP_M_WEIBULL_1(),
667  sipar_.METRX_F_DECOMP_M_WEIBULL_2(),
668  1.0));
669  return cbm::harmonic_mean2( fact_t, fact_m);
670 }
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◆ MeTrX_get_n_tot()

double ldndc::SoilChemistryMeTrX::MeTrX_get_n_tot ( )
private
Parameters
[in]None
[out]None
Returns
Total soil associated nitrogen

Referenced by MeTrX_get_c_tot().

19 {
20  double n_tot( n_algae + n_dead_algae + sc_.n_wood
21  + sc_.n_stubble_lit1 + sc_.n_stubble_lit2 + sc_.n_stubble_lit3
22  + sc_.n_raw_lit_1_above + sc_.n_raw_lit_2_above + sc_.n_raw_lit_3_above);
23 
24  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
25  {
26  n_tot += ( sc_.n_wood_sl[sl]
27  + nh4_ae_sl[sl] + nh4_an_sl[sl] + sc_.clay_nh4_sl[sl] + sc_.coated_nh4_sl[sl] + nh4_ice_sl[sl]
28  + sc_.nh3_liq_sl[sl] + sc_.nh3_gas_sl[sl] + sc_.urea_sl[sl]
29  + no3_ae_sl[sl] + no3_an_sl[sl] + no3_ice_sl[sl]
30  + sc_.no2_sl[sl] + sc_.an_no2_sl[sl]
31  + don_ae_sl[sl] + don_an_sl[sl] + don_ice_sl[sl]
32  + no_gas_sl[sl] + an_no_gas_sl[sl] + no_liq_sl[sl] + an_no_liq_sl[sl]
33  + n2o_gas_sl[sl] + an_n2o_gas_sl[sl] + n2o_liq_sl[sl] + an_n2o_liq_sl[sl]
34  + sc_.N_lit1_sl[sl] + sc_.N_lit2_sl[sl] + sc_.N_lit3_sl[sl]
35  + sc_.n_raw_lit_1_sl[sl] + sc_.n_raw_lit_2_sl[sl] + sc_.n_raw_lit_3_sl[sl]
36  + n_micro_1_sl[sl] + n_micro_2_sl[sl] + n_micro_3_sl[sl]
37  + sc_.N_aorg_sl[sl] + n_microbial_necromass_sl[sl]
38  + n_humus_1_sl[sl] + n_humus_2_sl[sl] + n_humus_3_sl[sl]);
39  }
40 
41  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
42  {
43  n_tot += sb_.nh4_sbl[sbl] + sb_.coated_nh4_sbl[sbl]
44  + sb_.no3_sbl[sbl] + sb_.don_sbl[sbl]
45  + sb_.nh3_sbl[sbl] + sb_.urea_sbl[sbl]
46  + sb_.n2o_sbl[sbl] + sb_.no_sbl[sbl];
47  }
48 
49  n_tot += nh3_fl.sum();
50 
51  return n_tot;
52 }
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◆ MeTrX_get_ph_wl()

double ldndc::SoilChemistryMeTrX::MeTrX_get_ph_wl ( )
private
Parameters
[in]None
[out]None
Returns
double

Referenced by MeTrX_nh3_nh4_equilibrium(), MeTrX_write_output_daily(), MeTrX_write_output_layer_daily(), and MeTrX_write_output_subdaily().

525 {
526  if ( cbm::flt_greater_zero( wc_.surface_water))
527  {
528  return cbm::bound( PH_SURFACE_WATER, PH_SURFACE_WATER + ph_delta_pab_wl + ph_delta_urea_wl, PH_MAX);
529  }
530  else
531  {
532  return 7.0;
533  }
534 }
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◆ MeTrX_groundwater_access()

void ldndc::SoilChemistryMeTrX::MeTrX_groundwater_access ( )
private
Parameters
[in]None
[out]None
Returns
void
  • exchange of soil no3 <-> groundwater no3
  • only calculated in case of valid groundwater input

References MeTrX_dissolution(), MeTrX_dissolution_soil(), MeTrX_ebullition(), MeTrX_gas_diffusion(), and MeTrX_liq_diffusion().

Referenced by solve().

539 {
540  if ( gw_ != NULL)
541  {
542  for ( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
543  {
544  if ( sc_.depth_sl[sl] > gw_->watertable_subday( lclock_ref()))
545  {
546  double const no3_gw( gw_->no3_day(lclock_ref()) //given in (mg no3 L-1)
547  * cbm::MN / (cbm::MN + 3.0 * cbm::MO) * cbm::KG_IN_MG //converts no3 from (mg no3) -> (kg n-no3)
548  * (wc_.wc_sl[sl] + wc_.ice_sl[sl]) * sc_.h_sl[sl] * cbm::DM3_IN_M3); //converts water (m3) -> (L)
549 
550  if ( cbm::flt_greater_zero( no3_gw))
551  {
552  double const no3_diff( GROUNDWATER_NUTRIENT_ACCESS_RATE * (no3_gw - no3_an_sl[sl]));
553  no3_an_sl[sl] += no3_diff;
554  day_no3_groundwater_access += no3_diff;
555  sc_.accumulated_no3_leach -= no3_diff;
556  sc_.accumulated_n_no3_leaching_sl[sl] -= no3_diff;
557  }
558  }
559  }
560 
561  if ( have_river_connection)
562  {
563  if ( have_water_table)
564  {
565  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
566  {
567  DISSOLUTION_ATMOSPHERE( MeTrX_get_atm_eq_liq( o2_atm_eq_liq, h_wl), sb_.o2_sbl[sbl], subdaily_o2_water[subdaily_time_step_]);
568  DISSOLUTION_ATMOSPHERE( MeTrX_get_atm_eq_liq( ch4_atm_eq_liq, h_wl), sb_.ch4_sbl[sbl], subdaily_ch4_water[subdaily_time_step_]);
569  DISSOLUTION_ATMOSPHERE( MeTrX_get_atm_eq_liq( co2_atm_eq_liq, h_wl), sb_.co2_sbl[sbl], subdaily_co2_water[subdaily_time_step_]);
570  DISSOLUTION_ATMOSPHERE( MeTrX_get_atm_eq_liq( nh3_atm_eq_liq, h_wl), sb_.nh3_sbl[sbl], subdaily_nh3_water[subdaily_time_step_]);
571  DISSOLUTION_ATMOSPHERE( MeTrX_get_atm_eq_liq( no_atm_eq_liq, h_wl), sb_.no_sbl[sbl], subdaily_no_water[subdaily_time_step_]);
572  DISSOLUTION_ATMOSPHERE( MeTrX_get_atm_eq_liq( n2o_atm_eq_liq, h_wl), sb_.n2o_sbl[sbl], subdaily_n2o_water[subdaily_time_step_]);
573  }
574  }
575  }
576  }
577 }
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◆ MeTrX_iron_oxidation()

void ldndc::SoilChemistryMeTrX::MeTrX_iron_oxidation ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_iron_reduction()

void ldndc::SoilChemistryMeTrX::MeTrX_iron_reduction ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_leaching()

void ldndc::SoilChemistryMeTrX::MeTrX_leaching ( )
private

Downwards transport of solutes, litter and humus with percolation water.

Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

25 {
26  /*************************/
27  /* Water table transport */
28  /*************************/
29 
30  if ( have_water_table &&
31  cbm::flt_greater_zero( infiltration))
32  {
33  ldndc_kassert( h_wl > 0.0);
34 
35  accumulated_n_nh4_infiltration_leach_sl[0] -= nh4_an_sl[0] + sc_.coated_nh4_sl[0];
36  accumulated_n_nh3_infiltration_leach_sl[0] -= sc_.nh3_liq_sl[0];
37  accumulated_n_no_infiltration_leach_sl[0] -= an_no_liq_sl[0];
38  accumulated_n_n2o_infiltration_leach_sl[0] -= an_n2o_liq_sl[0];
39  accumulated_n_urea_infiltration_leach_sl[0] -= sc_.urea_sl[0];
40  accumulated_n_no3_infiltration_leach_sl[0] -= no3_an_sl[0];
41  accumulated_n_don_infiltration_leach_sl[0] -= don_an_sl[0];
42 
43  double const leach_fact_sbl( cbm::bound_max( infiltration / h_wl, 0.99));
44  LEACH_DOWN( sb_.ch4_sbl[0], ch4_liq_sl[0], leach_fact_sbl);
45  LEACH_DOWN( sb_.o2_sbl[0], o2_liq_sl[0], leach_fact_sbl);
46  LEACH_DOWN( sb_.nh4_sbl[0], nh4_an_sl[0], leach_fact_sbl);
47  LEACH_DOWN( sb_.coated_nh4_sbl[0], sc_.coated_nh4_sl[0], leach_fact_sbl);
48  LEACH_DOWN( sb_.nh3_sbl[0], sc_.nh3_liq_sl[0], leach_fact_sbl);
49  LEACH_DOWN( sb_.no_sbl[0], an_no_liq_sl[0], leach_fact_sbl);
50  LEACH_DOWN( sb_.n2o_sbl[0], an_n2o_liq_sl[0], leach_fact_sbl);
51  LEACH_DOWN( sb_.urea_sbl[0], sc_.urea_sl[0], leach_fact_sbl);
52  LEACH_DOWN( sb_.no3_sbl[0], no3_an_sl[0], leach_fact_sbl);
53  LEACH_DOWN( sb_.don_sbl[0], don_an_sl[0], leach_fact_sbl);
54  LEACH_DOWN( sb_.doc_sbl[0], sc_.doc_sl[0], leach_fact_sbl);
55  LEACH_DOWN( sb_.co2_sbl[0], co2_liq_sl[0], leach_fact_sbl);
56  LEACH_DOWN( sb_.so4_sbl[0], sc_.so4_sl[0], leach_fact_sbl);
57  LEACH_DOWN( sb_.ni_sbl[0], sc_.ni_sl[0], leach_fact_sbl);
58 
59  accumulated_n_nh4_infiltration_leach_sl[0] += nh4_an_sl[0] + sc_.coated_nh4_sl[0];
60  accumulated_n_nh3_infiltration_leach_sl[0] += sc_.nh3_liq_sl[0];
61  accumulated_n_no_infiltration_leach_sl[0] += an_no_liq_sl[0];
62  accumulated_n_n2o_infiltration_leach_sl[0] += an_n2o_liq_sl[0];
63  accumulated_n_urea_infiltration_leach_sl[0] += sc_.urea_sl[0];
64  accumulated_n_no3_infiltration_leach_sl[0] += no3_an_sl[0];
65  accumulated_n_don_infiltration_leach_sl[0] += don_an_sl[0];
66 
67  for (size_t sbl = 1; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
68  {
69  size_t const sbl_plus( sbl - 1);
70  LEACH_DOWN( sb_.ch4_sbl[sbl], sb_.ch4_sbl[sbl_plus], leach_fact_sbl);
71  LEACH_DOWN( sb_.o2_sbl[sbl], sb_.o2_sbl[sbl_plus], leach_fact_sbl);
72  LEACH_DOWN( sb_.nh4_sbl[sbl], sb_.nh4_sbl[sbl_plus], leach_fact_sbl);
73  LEACH_DOWN( sb_.coated_nh4_sbl[sbl], sb_.coated_nh4_sbl[sbl_plus], leach_fact_sbl);
74  LEACH_DOWN( sb_.nh3_sbl[sbl], sb_.nh3_sbl[sbl_plus], leach_fact_sbl);
75  LEACH_DOWN( sb_.no_sbl[sbl], sb_.no_sbl[sbl_plus], leach_fact_sbl);
76  LEACH_DOWN( sb_.n2o_sbl[sbl], sb_.n2o_sbl[sbl_plus], leach_fact_sbl);
77  LEACH_DOWN( sb_.urea_sbl[sbl], sb_.urea_sbl[sbl_plus], leach_fact_sbl);
78  LEACH_DOWN( sb_.no3_sbl[sbl], sb_.no3_sbl[sbl_plus], leach_fact_sbl);
79  LEACH_DOWN( sb_.don_sbl[sbl], sb_.don_sbl[sbl_plus], leach_fact_sbl);
80  LEACH_DOWN( sb_.doc_sbl[sbl], sb_.doc_sbl[sbl_plus], leach_fact_sbl);
81  LEACH_DOWN( sb_.co2_sbl[sbl], sb_.co2_sbl[sbl_plus], leach_fact_sbl);
82  LEACH_DOWN( sb_.so4_sbl[sbl], sb_.so4_sbl[sbl_plus], leach_fact_sbl);
83  LEACH_DOWN( sb_.ni_sbl[sbl], sb_.ni_sbl[sbl_plus], leach_fact_sbl);
84  }
85  }
86 
87  /************************/
88  /* Soil water transport */
89  /************************/
90 
91  if ( cbm::flt_greater_zero( waterflux_sl[0]) &&
92  cbm::flt_greater_zero( v_water_sl[0]))
93  {
94  size_t const sl( 0);
95  size_t const sl_plus( 1);
96 
97  double const leach_fact( cbm::bound_min( 0.0, waterflux_sl[sl] / v_water_sl[sl]));
98 
99  double const leach_fact_nh4( cbm::bound_max( leach_fact * sipar_.RETNH4(), 0.9999));
100  double const leach_fact_no3( cbm::bound_max( leach_fact * sipar_.RETNO3(), 0.9999));
101  double const leach_fact_doc( cbm::bound_max( leach_fact * sipar_.RETDOC(), 0.9999));
102  double const leach_fact_mic( cbm::bound_max( leach_fact * sipar_.METRX_RET_MICROBES(), 0.9999));
103  double const leach_fact_lit( cbm::bound_max( leach_fact * sipar_.METRX_RET_LITTER(), 0.9999));
104  double const leach_fact_hum( cbm::bound_max( leach_fact * sipar_.METRX_RET_HUMUS(), 0.9999));
105  double const leach_fact_dissolved_gases( cbm::bound_max( leach_fact, 0.9999));
106 
107  accumulated_n_aorg_leaching_sl[sl] += sc_.N_aorg_sl[sl] * leach_fact_mic;
108  LEACH_DOWN( sc_.C_aorg_sl[sl], sc_.C_aorg_sl[sl_plus], leach_fact_mic);
109  LEACH_DOWN( sc_.N_aorg_sl[sl], sc_.N_aorg_sl[sl_plus], leach_fact_mic);
110 
111  transport_.leach_down_epsilon( sc_.C_micro1_sl[sl], sc_.C_micro1_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro1_sl[sl]));
112  transport_.leach_down_epsilon( sc_.C_micro2_sl[sl], sc_.C_micro2_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro2_sl[sl]));
113  transport_.leach_down_epsilon( sc_.C_micro3_sl[sl], sc_.C_micro3_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro3_sl[sl]));
114 
115  if( n_micro_1_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]) )
116  {
117  accumulated_n_micro_leaching_sl[sl] += ( n_micro_1_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]) ) * leach_fact_mic;
118  }
119  if( n_micro_2_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]) )
120  {
121  accumulated_n_micro_leaching_sl[sl] += ( n_micro_2_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]) ) * leach_fact_mic;
122  }
123  if( n_micro_3_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]) )
124  {
125  accumulated_n_micro_leaching_sl[sl] += ( n_micro_3_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]) ) * leach_fact_mic;
126  }
127  transport_.leach_down_epsilon( n_micro_1_sl[sl], n_micro_1_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]));
128  transport_.leach_down_epsilon( n_micro_2_sl[sl], n_micro_2_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]));
129  transport_.leach_down_epsilon( n_micro_3_sl[sl], n_micro_3_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]));
130 
131  LEACH_DOWN( sc_.C_lit1_sl[sl], sc_.C_lit1_sl[sl_plus], leach_fact_lit);
132  LEACH_DOWN( sc_.C_lit2_sl[sl], sc_.C_lit2_sl[sl_plus], leach_fact_lit);
133  LEACH_DOWN( sc_.C_lit3_sl[sl], sc_.C_lit3_sl[sl_plus], leach_fact_lit);
134 
135  accumulated_n_litter_leaching_sl[sl] += (sc_.N_lit1_sl[sl] + sc_.N_lit2_sl[sl] + sc_.N_lit3_sl[sl]) * leach_fact_lit;
136  LEACH_DOWN( sc_.N_lit1_sl[sl], sc_.N_lit1_sl[sl_plus], leach_fact_lit);
137  LEACH_DOWN( sc_.N_lit2_sl[sl], sc_.N_lit2_sl[sl_plus], leach_fact_lit);
138  LEACH_DOWN( sc_.N_lit3_sl[sl], sc_.N_lit3_sl[sl_plus], leach_fact_lit);
139 
140  LEACH_DOWN( c_humus_1_sl[sl], c_humus_1_sl[sl_plus], leach_fact_hum);
141  LEACH_DOWN( c_humus_2_sl[sl], c_humus_2_sl[sl_plus], leach_fact_hum);
142  LEACH_DOWN( c_humus_3_sl[sl], c_humus_3_sl[sl_plus], leach_fact_hum);
143 
144  accumulated_n_humus_1_leaching_sl[sl] += n_humus_1_sl[sl] * leach_fact_hum;
145  accumulated_n_humus_2_leaching_sl[sl] += n_humus_2_sl[sl] * leach_fact_hum;
146  accumulated_n_humus_3_leaching_sl[sl] += n_humus_3_sl[sl] * leach_fact_hum;
147  LEACH_DOWN( n_humus_1_sl[sl], n_humus_1_sl[sl_plus], leach_fact_hum);
148  LEACH_DOWN( n_humus_2_sl[sl], n_humus_2_sl[sl_plus], leach_fact_hum);
149  LEACH_DOWN( n_humus_3_sl[sl], n_humus_3_sl[sl_plus], leach_fact_hum);
150 
151  accumulated_n_nh4_leaching_sl[sl] += (nh4_ae_sl[sl] + nh4_an_sl[sl] + sc_.coated_nh4_sl[sl]) * leach_fact_nh4;
152  accumulated_n_nh3_leaching_sl[sl] += sc_.nh3_liq_sl[sl] * leach_fact_doc;
153  accumulated_n_urea_leaching_sl[sl] += sc_.urea_sl[sl] * leach_fact_doc;
154  LEACH_DOWN( nh4_ae_sl[sl], nh4_ae_sl[sl_plus], leach_fact_nh4);
155  LEACH_DOWN( nh4_an_sl[sl], nh4_an_sl[sl_plus], leach_fact_nh4);
156  LEACH_DOWN( sc_.coated_nh4_sl[sl], sc_.coated_nh4_sl[sl_plus], leach_fact_nh4);
157  LEACH_DOWN( sc_.nh3_liq_sl[sl], sc_.nh3_liq_sl[sl_plus], leach_fact_doc);
158  LEACH_DOWN( sc_.urea_sl[sl], sc_.urea_sl[sl_plus], leach_fact_doc);
159 
160  sc_.accumulated_n_no3_leaching_sl[sl] += (no3_ae_sl[sl] + no3_an_sl[sl]) * leach_fact_no3;
161  LEACH_DOWN( no3_ae_sl[sl], no3_ae_sl[sl_plus], leach_fact_no3);
162  LEACH_DOWN( no3_an_sl[sl], no3_an_sl[sl_plus], leach_fact_no3);
163 
164  accumulated_n_don_leaching_sl[sl] += (don_ae_sl[sl] + don_an_sl[sl]) * leach_fact_doc;
165  LEACH_DOWN( don_ae_sl[sl], don_ae_sl[sl_plus], leach_fact_doc);
166  LEACH_DOWN( don_an_sl[sl], don_an_sl[sl_plus], leach_fact_doc);
167  LEACH_DOWN( sc_.doc_sl[sl], sc_.doc_sl[sl_plus], leach_fact_doc);
168  LEACH_DOWN( sc_.an_doc_sl[sl], sc_.an_doc_sl[sl_plus], leach_fact_doc);
169  LEACH_DOWN( ae_acetate_sl[sl], ae_acetate_sl[sl_plus], leach_fact_doc);
170  LEACH_DOWN( an_acetate_sl[sl], an_acetate_sl[sl_plus], leach_fact_doc);
171 
172  accumulated_n_no_leaching_sl[sl] += (no_liq_sl[sl]+an_no_liq_sl[sl]) * leach_fact_dissolved_gases;
173  accumulated_n_n2o_leaching_sl[sl] += (n2o_liq_sl[sl]+an_n2o_liq_sl[sl]) * leach_fact_dissolved_gases;
174  LEACH_DOWN( no_liq_sl[sl], no_liq_sl[sl_plus], leach_fact_dissolved_gases);
175  LEACH_DOWN( an_no_liq_sl[sl], an_no_liq_sl[sl_plus], leach_fact_dissolved_gases);
176  LEACH_DOWN( n2o_liq_sl[sl], n2o_liq_sl[sl_plus], leach_fact_dissolved_gases);
177  LEACH_DOWN( an_n2o_liq_sl[sl], an_n2o_liq_sl[sl_plus], leach_fact_dissolved_gases);
178 
179  LEACH_DOWN( ch4_liq_sl[sl], ch4_liq_sl[sl_plus], leach_fact_dissolved_gases);
180  LEACH_DOWN( co2_liq_sl[sl], co2_liq_sl[sl_plus], leach_fact_dissolved_gases);
181  LEACH_DOWN( o2_liq_sl[sl], o2_liq_sl[sl_plus], leach_fact_dissolved_gases);
182 
183  LEACH_DOWN( sc_.so4_sl[sl], sc_.so4_sl[sl_plus], leach_fact_no3);
184  LEACH_DOWN( sc_.ni_sl[sl], sc_.ni_sl[sl_plus], leach_fact_doc);
185  }
186 
187  for( size_t sl = 1; sl < sl_.soil_layer_cnt()-1; ++sl)
188  {
189  if ( !cbm::flt_equal_zero( waterflux_sl[sl]) &&
190  cbm::flt_greater_zero( v_water_sl[sl]))
191  {
192  size_t sl_minus( sl - 1);
193  size_t sl_plus( sl + 1);
194 
195  double const leach_fact( waterflux_sl[sl] / v_water_sl[sl]);
196 
197  double const leach_fact_nh4( cbm::bound(-0.9999, leach_fact * sipar_.RETNH4(), 0.9999));
198  double const leach_fact_no3( cbm::bound(-0.9999, leach_fact * sipar_.RETNO3(), 0.9999));
199  double const leach_fact_doc( cbm::bound(-0.9999, leach_fact * sipar_.RETDOC(), 0.9999));
200  double const leach_fact_mic( cbm::bound(-0.9999, leach_fact * sipar_.METRX_RET_MICROBES(), 0.9999));
201  double const leach_fact_lit( cbm::bound(-0.9999, leach_fact * sipar_.METRX_RET_LITTER(), 0.9999));
202  double const leach_fact_hum( cbm::bound(-0.9999, leach_fact * sipar_.METRX_RET_HUMUS(), 0.9999));
203  double const leach_fact_dissolved_gases( cbm::bound(-0.9999, leach_fact, 0.9999));
204 
205  accumulated_n_aorg_leaching_sl[sl] += sc_.N_aorg_sl[sl] * leach_fact_mic;
206  transport_.leach_up_and_down( sc_.C_aorg_sl[sl_minus], sc_.C_aorg_sl[sl], sc_.C_aorg_sl[sl_plus], leach_fact_mic);
207  transport_.leach_up_and_down( sc_.N_aorg_sl[sl_minus], sc_.N_aorg_sl[sl], sc_.N_aorg_sl[sl_plus], leach_fact_mic);
208 
209  transport_.leach_up_and_down_epsilon( sc_.C_micro1_sl[sl_minus], sc_.C_micro1_sl[sl], sc_.C_micro1_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro1_sl[sl]));
210  transport_.leach_up_and_down_epsilon( sc_.C_micro2_sl[sl_minus], sc_.C_micro2_sl[sl], sc_.C_micro2_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro2_sl[sl]));
211  transport_.leach_up_and_down_epsilon( sc_.C_micro3_sl[sl_minus], sc_.C_micro3_sl[sl], sc_.C_micro3_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro3_sl[sl]));
212 
213  if( n_micro_1_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]) )
214  {
215  accumulated_n_micro_leaching_sl[sl] += ( n_micro_1_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]) ) * leach_fact_mic;
216  }
217  if( n_micro_2_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]) )
218  {
219  accumulated_n_micro_leaching_sl[sl] += ( n_micro_2_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]) ) * leach_fact_mic;
220  }
221  if( n_micro_3_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]) )
222  {
223  accumulated_n_micro_leaching_sl[sl] += ( n_micro_3_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]) ) * leach_fact_mic;
224  }
225  transport_.leach_up_and_down_epsilon( n_micro_1_sl[sl_minus], n_micro_1_sl[sl], n_micro_1_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]));
226  transport_.leach_up_and_down_epsilon( n_micro_2_sl[sl_minus], n_micro_2_sl[sl], n_micro_2_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]));
227  transport_.leach_up_and_down_epsilon( n_micro_3_sl[sl_minus], n_micro_3_sl[sl], n_micro_3_sl[sl_plus], leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]));
228 
229  transport_.leach_up_and_down( sc_.C_lit1_sl[sl_minus], sc_.C_lit1_sl[sl], sc_.C_lit1_sl[sl_plus], leach_fact_lit);
230  transport_.leach_up_and_down( sc_.C_lit2_sl[sl_minus], sc_.C_lit2_sl[sl], sc_.C_lit2_sl[sl_plus], leach_fact_lit);
231  transport_.leach_up_and_down( sc_.C_lit3_sl[sl_minus], sc_.C_lit3_sl[sl], sc_.C_lit3_sl[sl_plus], leach_fact_lit);
232 
233  accumulated_n_litter_leaching_sl[sl] += (sc_.N_lit1_sl[sl]+sc_.N_lit2_sl[sl]+sc_.N_lit3_sl[sl]) * leach_fact_lit;
234  transport_.leach_up_and_down( sc_.N_lit1_sl[sl_minus], sc_.N_lit1_sl[sl], sc_.N_lit1_sl[sl_plus], leach_fact_lit);
235  transport_.leach_up_and_down( sc_.N_lit2_sl[sl_minus], sc_.N_lit2_sl[sl], sc_.N_lit2_sl[sl_plus], leach_fact_lit);
236  transport_.leach_up_and_down( sc_.N_lit3_sl[sl_minus], sc_.N_lit3_sl[sl], sc_.N_lit3_sl[sl_plus], leach_fact_lit);
237 
238  transport_.leach_up_and_down( c_humus_1_sl[sl_minus], c_humus_1_sl[sl], c_humus_1_sl[sl_plus], leach_fact_hum);
239  transport_.leach_up_and_down( c_humus_2_sl[sl_minus], c_humus_2_sl[sl], c_humus_2_sl[sl_plus], leach_fact_hum);
240  transport_.leach_up_and_down( c_humus_3_sl[sl_minus], c_humus_3_sl[sl], c_humus_3_sl[sl_plus], leach_fact_hum);
241 
242  accumulated_n_humus_1_leaching_sl[sl] += n_humus_1_sl[sl] * leach_fact_hum;
243  accumulated_n_humus_2_leaching_sl[sl] += n_humus_2_sl[sl] * leach_fact_hum;
244  accumulated_n_humus_3_leaching_sl[sl] += n_humus_3_sl[sl] * leach_fact_hum;
245  transport_.leach_up_and_down( n_humus_1_sl[sl_minus], n_humus_1_sl[sl], n_humus_1_sl[sl_plus], leach_fact_hum);
246  transport_.leach_up_and_down( n_humus_2_sl[sl_minus], n_humus_2_sl[sl], n_humus_2_sl[sl_plus], leach_fact_hum);
247  transport_.leach_up_and_down( n_humus_3_sl[sl_minus], n_humus_3_sl[sl], n_humus_3_sl[sl_plus], leach_fact_hum);
248 
249  accumulated_n_nh4_leaching_sl[sl] += (nh4_ae_sl[sl] + nh4_an_sl[sl] + sc_.coated_nh4_sl[sl]) * leach_fact_nh4;
250  accumulated_n_nh3_leaching_sl[sl] += sc_.nh3_liq_sl[sl] * leach_fact_doc;
251  accumulated_n_urea_leaching_sl[sl] += sc_.urea_sl[sl] * leach_fact_doc;
252  transport_.leach_up_and_down( nh4_ae_sl[sl_minus], nh4_ae_sl[sl], nh4_ae_sl[sl_plus], leach_fact_nh4);
253  transport_.leach_up_and_down( nh4_an_sl[sl_minus], nh4_an_sl[sl], nh4_an_sl[sl_plus], leach_fact_nh4);
254  transport_.leach_up_and_down( sc_.coated_nh4_sl[sl_minus], sc_.coated_nh4_sl[sl], sc_.coated_nh4_sl[sl_plus], leach_fact_nh4);
255  transport_.leach_up_and_down( sc_.nh3_liq_sl[sl_minus], sc_.nh3_liq_sl[sl], sc_.nh3_liq_sl[sl_plus], leach_fact_doc);
256  transport_.leach_up_and_down( sc_.urea_sl[sl_minus], sc_.urea_sl[sl], sc_.urea_sl[sl_plus], leach_fact_doc);
257 
258  sc_.accumulated_n_no3_leaching_sl[sl] += (no3_ae_sl[sl]+no3_an_sl[sl]) * leach_fact_no3;
259  transport_.leach_up_and_down( no3_ae_sl[sl_minus], no3_ae_sl[sl], no3_ae_sl[sl_plus], leach_fact_no3);
260  transport_.leach_up_and_down( no3_an_sl[sl_minus], no3_an_sl[sl], no3_an_sl[sl_plus], leach_fact_no3);
261 
262  accumulated_n_don_leaching_sl[sl] += (don_ae_sl[sl] + don_an_sl[sl]) * leach_fact_doc;
263  transport_.leach_up_and_down( don_ae_sl[sl_minus], don_ae_sl[sl], don_ae_sl[sl_plus], leach_fact_doc);
264  transport_.leach_up_and_down( don_an_sl[sl_minus], don_an_sl[sl], don_an_sl[sl_plus], leach_fact_doc);
265  transport_.leach_up_and_down( sc_.doc_sl[sl_minus], sc_.doc_sl[sl], sc_.doc_sl[sl_plus], leach_fact_doc);
266  transport_.leach_up_and_down( sc_.an_doc_sl[sl_minus], sc_.an_doc_sl[sl], sc_.an_doc_sl[sl_plus], leach_fact_doc);
267  transport_.leach_up_and_down( ae_acetate_sl[sl_minus], ae_acetate_sl[sl], ae_acetate_sl[sl_plus], leach_fact_doc);
268  transport_.leach_up_and_down( an_acetate_sl[sl_minus], an_acetate_sl[sl], an_acetate_sl[sl_plus], leach_fact_doc);
269 
270  accumulated_n_no_leaching_sl[sl] += (no_liq_sl[sl]+an_no_liq_sl[sl]) * leach_fact_dissolved_gases;
271  accumulated_n_n2o_leaching_sl[sl] += (n2o_liq_sl[sl]+an_n2o_liq_sl[sl]) * leach_fact_dissolved_gases;
272  transport_.leach_up_and_down( no_liq_sl[sl_minus], no_liq_sl[sl], no_liq_sl[sl_plus], leach_fact_dissolved_gases);
273  transport_.leach_up_and_down( an_no_liq_sl[sl_minus], an_no_liq_sl[sl], an_no_liq_sl[sl_plus], leach_fact_dissolved_gases);
274  transport_.leach_up_and_down( n2o_liq_sl[sl_minus], n2o_liq_sl[sl], n2o_liq_sl[sl_plus], leach_fact_dissolved_gases);
275  transport_.leach_up_and_down( an_n2o_liq_sl[sl_minus], an_n2o_liq_sl[sl], an_n2o_liq_sl[sl_plus], leach_fact_dissolved_gases);
276 
277  transport_.leach_up_and_down( ch4_liq_sl[sl_minus], ch4_liq_sl[sl], ch4_liq_sl[sl_plus], leach_fact_dissolved_gases);
278  transport_.leach_up_and_down( co2_liq_sl[sl_minus], co2_liq_sl[sl], co2_liq_sl[sl_plus], leach_fact_dissolved_gases);
279  transport_.leach_up_and_down( o2_liq_sl[sl_minus], o2_liq_sl[sl], o2_liq_sl[sl_plus], leach_fact_dissolved_gases);
280 
281  transport_.leach_up_and_down( sc_.so4_sl[sl_minus], sc_.so4_sl[sl], sc_.so4_sl[sl_plus], leach_fact_no3);
282  transport_.leach_up_and_down( sc_.ni_sl[sl_minus], sc_.ni_sl[sl], sc_.ni_sl[sl_plus], leach_fact_doc);
283  }
284  }
285 
286  size_t sl( sl_.soil_layer_cnt()-1);
287 
288  if ( !cbm::flt_equal_zero( waterflux_sl[sl]) &&
289  cbm::flt_greater_zero( v_water_sl[sl]))
290  {
291  double dummy_out( 0.0); //dummy for substances that are not balanced (no accumulated leaching variable exists)
292  size_t sl_minus( sl_.soil_layer_cnt()-2);
293 
294  double const leach_fact( waterflux_sl[sl] / v_water_sl[sl]);
295 
296  double const leach_fact_nh4( cbm::bound(-0.9999, leach_fact * sipar_.RETNH4(), 0.9999));
297  double const leach_fact_no3( cbm::bound(-0.9999, leach_fact * sipar_.RETNO3(), 0.9999));
298  double const leach_fact_doc( cbm::bound(-0.9999, leach_fact * sipar_.RETDOC(), 0.9999));
299  double const leach_fact_mic( cbm::bound(-0.9999, leach_fact * sipar_.METRX_RET_MICROBES(), 0.9999));
300  double const leach_fact_lit( cbm::bound(-0.9999, leach_fact * sipar_.METRX_RET_LITTER(), 0.9999));
301  double const leach_fact_hum( cbm::bound(-0.9999, leach_fact * sipar_.METRX_RET_HUMUS(), 0.9999));
302  double const leach_fact_dissolved_gases( cbm::bound(-0.9999, leach_fact, 0.9999));
303 
304  accumulated_n_aorg_leaching_sl[sl] += sc_.N_aorg_sl[sl] * leach_fact_mic;
305  transport_.leach_up_and_down( sc_.C_aorg_sl[sl_minus], sc_.C_aorg_sl[sl], sc_.accumulated_doc_leach, leach_fact_mic);
306  transport_.leach_up_and_down( sc_.N_aorg_sl[sl_minus], sc_.N_aorg_sl[sl], sc_.accumulated_don_leach, leach_fact_mic);
307 
308  transport_.leach_up_and_down_epsilon( sc_.C_micro1_sl[sl_minus], sc_.C_micro1_sl[sl], sc_.accumulated_doc_leach, leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro1_sl[sl]));
309  transport_.leach_up_and_down_epsilon( sc_.C_micro2_sl[sl_minus], sc_.C_micro2_sl[sl], sc_.accumulated_doc_leach, leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro2_sl[sl]));
310  transport_.leach_up_and_down_epsilon( sc_.C_micro3_sl[sl_minus], sc_.C_micro3_sl[sl], sc_.accumulated_doc_leach, leach_fact_mic, MeTrX_get_micro_c_decay_max( sc_.C_micro3_sl[sl]));
311 
312  if( n_micro_1_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]) )
313  {
314  accumulated_n_micro_leaching_sl[sl] += ( n_micro_1_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]) ) * leach_fact_mic;
315  }
316  if( n_micro_2_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]) )
317  {
318  accumulated_n_micro_leaching_sl[sl] += ( n_micro_2_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]) ) * leach_fact_mic;
319  }
320  if( n_micro_3_sl[sl] > MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]) )
321  {
322  accumulated_n_micro_leaching_sl[sl] += ( n_micro_3_sl[sl] - MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]) ) * leach_fact_mic;
323  }
324  transport_.leach_up_and_down_epsilon( n_micro_1_sl[sl_minus], n_micro_1_sl[sl], sc_.accumulated_don_leach, leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_1_sl[sl]));
325  transport_.leach_up_and_down_epsilon( n_micro_2_sl[sl_minus], n_micro_2_sl[sl], sc_.accumulated_don_leach, leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_2_sl[sl]));
326  transport_.leach_up_and_down_epsilon( n_micro_3_sl[sl_minus], n_micro_3_sl[sl], sc_.accumulated_don_leach, leach_fact_mic, MeTrX_get_micro_n_decay_max( n_micro_3_sl[sl]));
327 
328  transport_.leach_up_and_down( sc_.C_lit1_sl[sl_minus], sc_.C_lit1_sl[sl], sc_.accumulated_doc_leach, leach_fact_lit);
329  transport_.leach_up_and_down( sc_.C_lit2_sl[sl_minus], sc_.C_lit2_sl[sl], sc_.accumulated_doc_leach, leach_fact_lit);
330  transport_.leach_up_and_down( sc_.C_lit3_sl[sl_minus], sc_.C_lit3_sl[sl], sc_.accumulated_doc_leach, leach_fact_lit);
331 
332  accumulated_n_litter_leaching_sl[sl] += (sc_.N_lit1_sl[sl]+sc_.N_lit2_sl[sl]+sc_.N_lit3_sl[sl]) * leach_fact_lit;
333  transport_.leach_up_and_down( sc_.N_lit1_sl[sl_minus], sc_.N_lit1_sl[sl], sc_.accumulated_don_leach, leach_fact_lit);
334  transport_.leach_up_and_down( sc_.N_lit2_sl[sl_minus], sc_.N_lit2_sl[sl], sc_.accumulated_don_leach, leach_fact_lit);
335  transport_.leach_up_and_down( sc_.N_lit3_sl[sl_minus], sc_.N_lit3_sl[sl], sc_.accumulated_don_leach, leach_fact_lit);
336 
337  transport_.leach_up_and_down( c_humus_1_sl[sl_minus], c_humus_1_sl[sl], sc_.accumulated_doc_leach, leach_fact_hum);
338  transport_.leach_up_and_down( c_humus_2_sl[sl_minus], c_humus_2_sl[sl], sc_.accumulated_doc_leach, leach_fact_hum);
339  transport_.leach_up_and_down( c_humus_3_sl[sl_minus], c_humus_3_sl[sl], sc_.accumulated_doc_leach, leach_fact_hum);
340 
341  accumulated_n_humus_1_leaching_sl[sl] += n_humus_1_sl[sl] * leach_fact_hum;
342  accumulated_n_humus_2_leaching_sl[sl] += n_humus_2_sl[sl] * leach_fact_hum;
343  accumulated_n_humus_3_leaching_sl[sl] += n_humus_3_sl[sl] * leach_fact_hum;
344  transport_.leach_up_and_down( n_humus_1_sl[sl_minus], n_humus_1_sl[sl], sc_.accumulated_don_leach, leach_fact_hum);
345  transport_.leach_up_and_down( n_humus_2_sl[sl_minus], n_humus_2_sl[sl], sc_.accumulated_don_leach, leach_fact_hum);
346  transport_.leach_up_and_down( n_humus_2_sl[sl_minus], n_humus_2_sl[sl], sc_.accumulated_don_leach, leach_fact_hum);
347 
348  accumulated_n_nh4_leaching_sl[sl] += (nh4_ae_sl[sl] + nh4_an_sl[sl] + sc_.coated_nh4_sl[sl]) * leach_fact_nh4;
349  accumulated_n_nh3_leaching_sl[sl] += sc_.nh3_liq_sl[sl] * leach_fact_doc;
350  accumulated_n_urea_leaching_sl[sl] += sc_.urea_sl[sl] * leach_fact_doc;
351  transport_.leach_up_and_down( nh4_ae_sl[sl_minus], nh4_ae_sl[sl], sc_.accumulated_nh4_leach, leach_fact_nh4);
352  transport_.leach_up_and_down( nh4_an_sl[sl_minus], nh4_an_sl[sl], sc_.accumulated_nh4_leach, leach_fact_nh4);
353  transport_.leach_up_and_down( sc_.coated_nh4_sl[sl_minus], sc_.coated_nh4_sl[sl], sc_.accumulated_nh4_leach, leach_fact_nh4);
354  transport_.leach_up_and_down( sc_.nh3_liq_sl[sl_minus], sc_.nh3_liq_sl[sl], day_leach_nh3, leach_fact_doc);
355  transport_.leach_up_and_down( sc_.urea_sl[sl_minus], sc_.urea_sl[sl], day_leach_urea, leach_fact_doc);
356 
357  sc_.accumulated_n_no3_leaching_sl[sl] += (no3_ae_sl[sl]+no3_an_sl[sl]) * leach_fact_no3;
358  transport_.leach_up_and_down( no3_ae_sl[sl_minus], no3_ae_sl[sl], sc_.accumulated_no3_leach, leach_fact_no3);
359  transport_.leach_up_and_down( no3_an_sl[sl_minus], no3_an_sl[sl], sc_.accumulated_no3_leach, leach_fact_no3);
360 
361  accumulated_n_don_leaching_sl[sl] += (don_ae_sl[sl] + don_an_sl[sl]) * leach_fact_doc;
362  transport_.leach_up_and_down( don_ae_sl[sl_minus], don_ae_sl[sl], sc_.accumulated_don_leach, leach_fact_doc);
363  transport_.leach_up_and_down( don_an_sl[sl_minus], don_an_sl[sl], sc_.accumulated_don_leach, leach_fact_doc);
364  transport_.leach_up_and_down( sc_.doc_sl[sl_minus], sc_.doc_sl[sl], sc_.accumulated_doc_leach, leach_fact_doc);
365  transport_.leach_up_and_down( sc_.an_doc_sl[sl_minus], sc_.an_doc_sl[sl], sc_.accumulated_doc_leach, leach_fact_doc);
366  transport_.leach_up_and_down( ae_acetate_sl[sl_minus], ae_acetate_sl[sl], sc_.accumulated_doc_leach, leach_fact_doc);
367  transport_.leach_up_and_down( an_acetate_sl[sl_minus], an_acetate_sl[sl], sc_.accumulated_doc_leach, leach_fact_doc);
368 
369  accumulated_n_no_leaching_sl[sl] += (no_liq_sl[sl]+an_no_liq_sl[sl]) * leach_fact_dissolved_gases;
370  accumulated_n_n2o_leaching_sl[sl] += (n2o_liq_sl[sl]+an_n2o_liq_sl[sl]) * leach_fact_dissolved_gases;
371  transport_.leach_up_and_down( no_liq_sl[sl_minus], no_liq_sl[sl], day_leach_no, leach_fact_dissolved_gases);
372  transport_.leach_up_and_down( an_no_liq_sl[sl_minus], an_no_liq_sl[sl], day_leach_no, leach_fact_dissolved_gases);
373  transport_.leach_up_and_down( n2o_liq_sl[sl_minus], n2o_liq_sl[sl], day_leach_n2o, leach_fact_dissolved_gases);
374  transport_.leach_up_and_down( an_n2o_liq_sl[sl_minus], an_n2o_liq_sl[sl], day_leach_n2o, leach_fact_dissolved_gases);
375  transport_.leach_up_and_down( o2_liq_sl[sl_minus], o2_liq_sl[sl], day_leach_o2, leach_fact_dissolved_gases);
376 
377  transport_.leach_up_and_down( ch4_liq_sl[sl_minus], ch4_liq_sl[sl], subdaily_ch4_leach[subdaily_time_step_], leach_fact_dissolved_gases);
378  transport_.leach_up_and_down( co2_liq_sl[sl_minus], co2_liq_sl[sl], subdaily_co2_leach[subdaily_time_step_], leach_fact_dissolved_gases);
379 
380  transport_.leach_up_and_down( sc_.so4_sl[sl_minus], sc_.so4_sl[sl], sc_.accumulated_so4_leach, leach_fact_no3);
381  transport_.leach_up_and_down( sc_.ni_sl[sl_minus], sc_.ni_sl[sl], dummy_out, leach_fact_doc);
382  }
383 }
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◆ MeTrX_liq_diffusion()

void ldndc::SoilChemistryMeTrX::MeTrX_liq_diffusion ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by MeTrX_groundwater_access(), and solve().

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◆ MeTrX_manure()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_manure ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by solve().

262 {
263  EventAttributes const * ev_manure = NULL;
264  while (( ev_manure = this->m_ManureEvents.pop()) != NULL)
265  {
266  double new_manure_n( -sc_.accumulated_n_fertilizer);
267  double new_manure_c( -sc_.accumulated_c_fertilizer);
268 
269  double me_c = ev_manure->get( "/carbon", -1.0);
270  if ( cbm::flt_less( me_c, 0.0))
271  {
272  KLOGERROR( "manure event: carbon and nitrogen amount must be greater 0",
273  " [carbon=",me_c,"]");
274  return LDNDC_ERR_FAIL;
275  }
276  double me_cn = ev_manure->get( "/carbon-nitrogen-ratio", -1.0);
277  if ( cbm::flt_less( me_cn, 0.0))
278  {
279  KLOGERROR( "manure event: carbon/nitrogen ratio must be greater 0",
280  " [carbon/nitrogen ratio=",me_cn,"]");
281  return LDNDC_ERR_FAIL;
282  }
283 
284  double add_c( me_c * cbm::HA_IN_M2);
285  double add_n( add_c / me_cn);
286 
287  sc_.accumulated_c_fertilizer += add_c;
288  sc_.accumulated_n_fertilizer += add_n;
289 
290  double add_n_nh4( 0.0);
291  double add_n_no3( 0.0);
292  double add_n_don( 0.0);
293  double add_n_urea( 0.0);
294 
295  double add_c_doc( 0.0);
296 
297  double add_c_aorg( 0.0);
298  double add_n_aorg( 0.0);
299 
300  double add_c_lit_1( 0.0);
301  double add_c_lit_2( 0.0);
302  double add_c_lit_3( 0.0);
303 
304  double add_n_lit_1( 0.0);
305  double add_n_lit_2( 0.0);
306  double add_n_lit_3( 0.0);
307 
308  double ph_manure = ev_manure->get( "/ph", -1.0);
309 
310  cbm::string_t const & manure = ev_manure->get( "/type", "-");
311  if ( manure == "slurry" )
312  {
313  double const avail_n = ev_manure->get( "/nitrogen-available", sipar_.FRAC_LABILE_N_SLURRY());
314  if ( !cbm::flt_greater_zero( avail_n))
315  {
316  KLOGERROR( "manure event (",manure,"): fraction of available nitrogen must be at least 0",
317  " [available nitrogen=",avail_n,"]");
318  return LDNDC_ERR_FAIL;
319  }
320  double const avail_c = ev_manure->get( "/carbon-available", sipar_.FRAC_LABILE_C_SLURRY());
321  if ( !cbm::flt_greater_zero( avail_c))
322  {
323  KLOGERROR( "manure event (",manure,"): fraction of available carbon must be at least 0",
324  " [available carbon=",avail_c,"]");
325  return LDNDC_ERR_FAIL;
326  }
327 
328  double const liq_n = avail_n * add_n;
329  double const f_urea = ev_manure->get( "/urea-fraction", sipar_.LIQUREA_SLURRY());
330  add_n_urea = f_urea * liq_n;
331  double const f_nh4 = ev_manure->get( "/nh4-fraction", sipar_.LIQNH4_SLURRY());
332  add_n_nh4 = f_nh4 * liq_n;
333  double const f_don = ev_manure->get( "/don-fraction", sipar_.LIQDON_SLURRY());
334  add_n_don = f_don * liq_n;
335  double const f_no3 = ev_manure->get( "/no3-fraction", sipar_.LIQNO3_SLURRY());
336  add_n_no3 = f_no3 * liq_n;
337 
338  if (cbm::flt_not_equal_zero( add_n_urea + add_n_nh4 + add_n_don + add_n_no3 - liq_n))
339  {
340  KLOGERROR( "manure event (",manure,"): fractions of liquid nitrogen do not add up to 1.0!",
341  " check UREA fraction, NH4 fraction, DON fraction and NO3 fraction");
342  return LDNDC_ERR_FAIL;
343  }
344 
345  add_c_doc = avail_c * add_c;
346 
347  double const add_c_res( add_c - add_c_doc);
348  double const add_n_res( add_n - add_n_don - add_n_nh4 - add_n_no3 - add_n_urea);
349 
350  double const f_lignin = ev_manure->get( "/lignin-fraction", 0.2); // Bhogal et al. (2011), Levi-Minzi et al. (1986), Probert et al. (2005)
351  double const frac_c_lit_3( f_lignin);
352  double const f_cellulose = ev_manure->get( "/cellulose-fraction", 0.6); // Bhogal et al. (2011), Levi-Minzi et al. (1986)
353  double const frac_c_lit_2( f_cellulose);
354  double const frac_c_lit_1( 1.0 - frac_c_lit_2 - frac_c_lit_3);
355 
356  if (( f_lignin + f_cellulose) > 1.0)
357  {
358  KLOGERROR( "manure event (",manure,"): fractions of litter do not add up to 1.0!",
359  " check lignin fraction and cellulose fraction");
360  return LDNDC_ERR_FAIL;
361  }
362 
363  add_c_lit_1 += ( frac_c_lit_1 * add_c_res);
364  add_c_lit_2 += ( frac_c_lit_2 * add_c_res);
365  add_c_lit_3 += ( frac_c_lit_3 * add_c_res);
366 
367  add_n_lit_1 += ( frac_c_lit_1 * add_n_res);
368  add_n_lit_2 += ( frac_c_lit_2 * add_n_res);
369  add_n_lit_3 += ( frac_c_lit_3 * add_n_res);
370  }
371  else if ( manure == "green" )
372  {
373  add_c_lit_1 = 0.2 * add_c;
374  add_c_lit_2 = 0.7 * add_c;
375  add_c_lit_3 = 0.1 * add_c;
376 
377  add_n_lit_1 = 0.2 * add_n;
378  add_n_lit_2 = 0.7 * add_n;
379  add_n_lit_3 = 0.1 * add_n;
380  }
381  else if ( manure == "straw" )
382  {
383  add_c_lit_1 = 0.2 * add_c;
384  add_c_lit_2 = 0.7 * add_c;
385  add_c_lit_3 = 0.1 * add_c;
386 
387  add_n_lit_1 = 0.2 * add_n;
388  add_n_lit_2 = 0.7 * add_n;
389  add_n_lit_3 = 0.1 * add_n;
390  }
391  else if ( manure == "farmyard" )
392  {
393  double const avail_n = ev_manure->get( "/nitrogen-available", sipar_.FRAC_LABILE_N_FARMYARD());
394  if ( !cbm::flt_greater_zero( avail_n))
395  {
396  KLOGERROR( "manure event (",manure,"): fraction of available nitrogen must be at least 0",
397  " [available nitrogen=",avail_n,"]");
398  return LDNDC_ERR_FAIL;
399  }
400  double const avail_c = ev_manure->get( "/carbon-available", sipar_.FRAC_LABILE_C_FARMYARD());
401  if ( !cbm::flt_greater_zero( avail_c))
402  {
403  KLOGERROR( "manure event (",manure,"): fraction of available carbon must be at least 0",
404  " [available carbon=",avail_c,"]");
405  return LDNDC_ERR_FAIL;
406  }
407 
408  double const liq_n = avail_n * add_n;
409  double const f_urea = ev_manure->get( "/urea-fraction", sipar_.LIQUREA_FARMYARD());
410  add_n_urea = f_urea * liq_n;
411  double const f_nh4 = ev_manure->get( "/nh4-fraction", sipar_.LIQNH4_FARMYARD());
412  add_n_nh4 = f_nh4 * liq_n;
413  double const f_don = ev_manure->get( "/don-fraction", sipar_.LIQDON_FARMYARD());
414  add_n_don = f_don * liq_n;
415  double const f_no3 = ev_manure->get( "/no3-fraction", sipar_.LIQNO3_FARMYARD());
416  add_n_no3 = f_no3 * liq_n;
417 
418  if (cbm::flt_not_equal_zero( add_n_urea + add_n_nh4 + add_n_don + add_n_no3 - liq_n))
419  {
420  KLOGERROR( "manure event (",manure,"): fractions of liquid nitrogen do not add up to 1.0!",
421  " check UREA fraction, NH4 fraction, DON fraction and NO3 fraction");
422  return LDNDC_ERR_FAIL;
423  }
424 
425  add_c_doc = avail_c * add_c;
426 
427  double const add_c_res( add_c - add_c_doc);
428  double const add_n_res( add_n - add_n_don - add_n_nh4 - add_n_no3 - add_n_urea);
429 
430  double const f_lignin = ev_manure->get( "/lignin-fraction", 0.2); // Bhogal et al. (2011), Levi-Minzi et al. (1986), Probert et al. (2005)
431  double const frac_c_lit_3( f_lignin);
432  double const f_cellulose = ev_manure->get( "/cellulose-fraction", 0.6); // Bhogal et al. (2011), Levi-Minzi et al. (1986)
433  double const frac_c_lit_2( f_cellulose);
434  double const frac_c_lit_1( 1.0 - frac_c_lit_2 - frac_c_lit_3);
435 
436  if (( f_lignin + f_cellulose) > 1.0)
437  {
438  KLOGERROR( "manure event (",manure,"): fractions of litter do not add up to 1.0!",
439  " check lignin fraction and cellulose fraction");
440  return LDNDC_ERR_FAIL;
441  }
442 
443  add_c_lit_1 += ( frac_c_lit_1 * add_c_res);
444  add_c_lit_2 += ( frac_c_lit_2 * add_c_res);
445  add_c_lit_3 += ( frac_c_lit_3 * add_c_res);
446 
447  add_n_lit_1 += ( frac_c_lit_1 * add_n_res);
448  add_n_lit_2 += ( frac_c_lit_2 * add_n_res);
449  add_n_lit_3 += ( frac_c_lit_3 * add_n_res);
450  }
451  else if ( manure == "compost" )
452  {
453  double const avail_n = ev_manure->get( "/nitrogen-available", sipar_.FRAC_LABILE_N_COMPOST());
454  if ( avail_n < 0.0)
455  {
456  KLOGERROR( "manure event (",manure,"): fraction of available nitrogen must be at least 0",
457  " [available nitrogen=",avail_n,"]");
458  return LDNDC_ERR_FAIL;
459  }
460  double const avail_c = ev_manure->get( "/carbon-available", sipar_.FRAC_LABILE_C_COMPOST());
461  if ( avail_c < 0.0)
462  {
463  KLOGERROR( "manure event (",manure,"): fraction of available carbon must be at least 0",
464  " [available carbon=",avail_c,"]");
465  return LDNDC_ERR_FAIL;
466  }
467 
468  double const liq_n = avail_n * add_n;
469  double const f_urea = ev_manure->get( "/urea-fraction", sipar_.LIQUREA_COMPOST());
470  add_n_urea = f_urea * liq_n;
471  double const f_nh4 = ev_manure->get( "/nh4-fraction", sipar_.LIQNH4_COMPOST());
472  add_n_nh4 = f_nh4 * liq_n;
473  double const f_don = ev_manure->get( "/don-fraction", sipar_.LIQDON_COMPOST());
474  add_n_don = f_don * liq_n;
475  double const f_no3 = ev_manure->get( "/no3-fraction", sipar_.LIQNO3_COMPOST());
476  add_n_no3 = f_no3 * liq_n;
477 
478  if (cbm::flt_not_equal_zero( add_n_urea+add_n_nh4+add_n_don+add_n_no3-liq_n))
479  {
480  KLOGERROR( "manure event (",manure,"): fractions of liquid nitrogen do not add up to 1.0!",
481  " check UREA fraction, NH4 fraction, DON fraction and NO3 fraction");
482  return LDNDC_ERR_FAIL;
483  }
484 
485  add_c_doc = ( avail_c * add_c);
486 
487  double const add_c_res( add_c - add_c_doc);
488  double const add_n_res( add_n - add_n_don - add_n_nh4 - add_n_no3 - add_n_urea);
489 
490  double const f_lignin = ev_manure->get( "/lignin-fraction", 0.8);
491  double const frac_c_lit_3( f_lignin);
492  double const f_cellulose = ev_manure->get( "/cellulose-fraction", 0.1);
493  double const frac_c_lit_2( f_cellulose);
494  double const frac_c_lit_1( 1.0 - frac_c_lit_2 - frac_c_lit_3);
495 
496  if (( f_lignin + f_cellulose) > 1.0)
497  {
498  KLOGERROR( "manure event (",manure,"): fractions of litter do not add up to 1.0!",
499  " check lignin fraction and cellulose fraction");
500  return LDNDC_ERR_FAIL;
501  }
502 
503  add_c_lit_1 += ( frac_c_lit_1 * add_c_res);
504  add_c_lit_2 += ( frac_c_lit_2 * add_c_res);
505  add_c_lit_3 += ( frac_c_lit_3 * add_c_res);
506 
507  add_n_lit_1 += ( frac_c_lit_1 * add_n_res);
508  add_n_lit_2 += ( frac_c_lit_2 * add_n_res);
509  add_n_lit_3 += ( frac_c_lit_3 * add_n_res);
510  }
511  else if ( manure == "generic" )
512  {
513  double const avail_n_default( (sipar_.FRAC_LABILE_N_SLURRY() + sipar_.FRAC_LABILE_N_FARMYARD()) / 2.0);
514  double const avail_n = ev_manure->get( "/nitrogen-available", avail_n_default);
515  if ( !cbm::flt_greater_zero( avail_n))
516  {
517  KLOGERROR( "manure event (",manure,"): fraction of available nitrogen must be at least 0",
518  " [available nitrogen=",avail_n,"]");
519  return LDNDC_ERR_FAIL;
520  }
521  double const avail_c_default( (sipar_.FRAC_LABILE_C_SLURRY() + sipar_.FRAC_LABILE_C_FARMYARD()) / 2.0);
522  double const avail_c = ev_manure->get( "/carbon-available", avail_c_default);
523  if ( !cbm::flt_greater_zero( avail_c))
524  {
525  KLOGERROR( "manure event (",manure,"): fraction of available carbon must be at least 0",
526  " [available carbon=",avail_c,"]");
527  return LDNDC_ERR_FAIL;
528  }
529 
530  double const liq_n = avail_n * add_n;
531 
532  double const f_urea_default( (sipar_.LIQUREA_SLURRY() + sipar_.LIQUREA_FARMYARD()) / 2.0);
533  double const f_urea = ev_manure->get( "/urea-fraction", f_urea_default);
534  add_n_urea = f_urea * liq_n;
535 
536  double const f_nh4_default( (sipar_.LIQNH4_SLURRY() + sipar_.LIQNH4_FARMYARD()) / 2.0);
537  double const f_nh4 = ev_manure->get( "/nh4-fraction", f_nh4_default);
538  add_n_nh4 = f_nh4 * liq_n;
539 
540  double const f_don_default( (sipar_.LIQDON_SLURRY() + sipar_.LIQDON_FARMYARD()) / 2.0);
541  double const f_don = ev_manure->get( "/don-fraction", f_don_default);
542  add_n_don = f_don * liq_n;
543 
544  double const f_no3_default( (sipar_.LIQNO3_SLURRY() + sipar_.LIQNO3_FARMYARD()) / 2.0);
545  double const f_no3 = ev_manure->get( "/no3-fraction", f_no3_default);
546  add_n_no3 = f_no3 * liq_n;
547 
548  if (cbm::flt_not_equal_zero( add_n_urea + add_n_nh4 + add_n_don + add_n_no3 - liq_n))
549  {
550  KLOGERROR( "manure event (",manure,"): fractions of liquid nitrogen do not add up to 1.0!",
551  " check UREA fraction, NH4 fraction, DON fraction and NO3 fraction");
552  return LDNDC_ERR_FAIL;
553  }
554 
555  add_c_doc = avail_c * add_c;
556 
557  double const add_c_res( add_c - add_c_doc);
558  double const add_n_res( add_n - add_n_don - add_n_nh4 - add_n_no3 - add_n_urea);
559 
560  double const f_lignin = ev_manure->get( "/lignin-fraction", 0.2);
561  double const frac_c_lit_3( f_lignin);
562  double const f_cellulose = ev_manure->get( "/cellulose-fraction", 0.6);
563  double const frac_c_lit_2( f_cellulose);
564  double const frac_c_lit_1( 1.0 - frac_c_lit_2 - frac_c_lit_3);
565 
566  if (( f_lignin + f_cellulose) > 1.0)
567  {
568  KLOGERROR( "manure event (",manure,"): fractions of litter do not add up to 1.0!",
569  " check lignin fraction and cellulose fraction");
570  return LDNDC_ERR_FAIL;
571  }
572 
573  add_c_lit_1 += ( frac_c_lit_1 * add_c_res);
574  add_c_lit_2 += ( frac_c_lit_2 * add_c_res);
575  add_c_lit_3 += ( frac_c_lit_3 * add_c_res);
576 
577  add_n_lit_1 += ( frac_c_lit_1 * add_n_res);
578  add_n_lit_2 += ( frac_c_lit_2 * add_n_res);
579  add_n_lit_3 += ( frac_c_lit_3 * add_n_res);
580  }
581  else
582  {
583  KLOGWARN( "Unknown manure type \"",manure,"\". Skipping event!");
584  break;
585  }
586 
587  double const depth( ev_manure->get( "/depth", 0.0));
588 
589  size_t l_0 = 0;
590  size_t l_1 = 1;
591  if ( cbm::flt_equal_zero( depth))
592  {
593  l_0 = 0;
594  l_1 = 1;
595  for( size_t sl = 1; sl < sl_.soil_layer_cnt(); ++sl)
596  {
597  if ( sc_.depth_sl[sl] <= 0.01)
598  {
599  l_1 = sl;
600  }
601  else
602  {
603  break;
604  }
605  }
606  }
607  else
608  {
609  //l_0 not allowed to be deeper than last but one soil layer
610  l_0 = sl_.soil_layer_cnt()-2;
611  //find first layer (from top) having at least depth <depth(fert)>
612  for ( size_t l = 0; l < sl_.soil_layer_cnt()-1; ++l)
613  {
614  if ( cbm::flt_greater_equal( sc_.depth_sl[l], depth))
615  {
616  l_0 = l;
617  break;
618  }
619  }
620  //l_1 must at least one layer below l_0
621  l_1 = l_0 + 1;
622  for ( size_t l = l_0 + 1; l < sl_.soil_layer_cnt(); ++l)
623  {
624  /* distribute at least among 4cm soil profile */
625  if ( cbm::flt_greater_equal( sc_.depth_sl[l], depth + 0.04))
626  {
627  l_1 = l;
628  break;
629  }
630  }
631  }
632 
633  for ( size_t sl = l_0; sl < l_1; ++sl)
634  {
635  double const layer_fraction( 1.0 / double(l_1 - l_0));
636  if ( cbm::flt_greater_zero( ph_manure))
637  {
638  sc_.ph_sl[sl] = ph_manure;
639  }
640  double const layer_fraction_ae( (1.0 - sc_.anvf_sl[sl]) * layer_fraction);
641  double const layer_fraction_an( sc_.anvf_sl[sl] * layer_fraction);
642 
643  don_ae_sl[sl] += add_n_don * layer_fraction_ae;
644  don_an_sl[sl] += add_n_don * layer_fraction_an;
645  nh4_ae_sl[sl] += add_n_nh4 * layer_fraction_ae;
646  nh4_an_sl[sl] += add_n_nh4 * layer_fraction_an;
647  no3_ae_sl[sl] += add_n_no3 * layer_fraction_ae;
648  no3_an_sl[sl] += add_n_no3 * layer_fraction_an;
649  sc_.urea_sl[sl] += add_n_urea * layer_fraction;
650 
651  sc_.doc_sl[sl] += add_c_doc * layer_fraction_ae;
652  sc_.an_doc_sl[sl] += add_c_doc * layer_fraction_an;
653 
654  sc_.C_aorg_sl[sl] += add_c_aorg * layer_fraction;
655  sc_.N_aorg_sl[sl] += add_n_aorg * layer_fraction;
656 
657  sc_.C_lit1_sl[sl] += add_c_lit_1 * layer_fraction;
658  sc_.C_lit2_sl[sl] += add_c_lit_2 * layer_fraction;
659  sc_.C_lit3_sl[sl] += add_c_lit_3 * layer_fraction;
660 
661  sc_.N_lit1_sl[sl] += add_n_lit_1 * layer_fraction;
662  sc_.N_lit2_sl[sl] += add_n_lit_2 * layer_fraction;
663  sc_.N_lit3_sl[sl] += add_n_lit_3 * layer_fraction;
664 
665  accumulated_n_nh4_fertilization_sl[sl] += add_n_nh4 * layer_fraction;
666  accumulated_n_no3_fertilization_sl[sl] += add_n_no3 * layer_fraction;
667  accumulated_n_don_fertilization_sl[sl] += add_n_don * layer_fraction;
668  accumulated_n_urea_fertilization_sl[sl] += add_n_urea * layer_fraction;
669  accumulated_n_litter_fertilization_sl[sl] += (add_n_lit_1 + add_n_lit_2 + add_n_lit_3) * layer_fraction;
670  accumulated_n_aorg_fertilization_sl[sl] += add_n_aorg * layer_fraction;
671  }
672 
673  cbm::state_scratch_t * mcom = io_kcomm->get_scratch();
674 
675  new_manure_n += sc_.accumulated_n_fertilizer;
676  double old_manure_n( 0.0);
677  mcom->get( "manure:amountN", &old_manure_n, 0.0);
678  mcom->set( "manure:amountN", old_manure_n + (new_manure_n * cbm::M2_IN_HA));
679 
680  new_manure_c += sc_.accumulated_c_fertilizer;
681  double old_manure_c( 0.0);
682  mcom->get( "manure:amountC", &old_manure_c, 0.0);
683  mcom->set( "manure:amountC", old_manure_c + (new_manure_c * cbm::M2_IN_HA));
684  }
685 
686  return LDNDC_ERR_OK;
687 }
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◆ MeTrX_metabolism()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_metabolism ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by solve().

188 {
189  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
190  {
191  double const metabolism_rate( 0.1 * FTS_TOT_);
192 
193  double const mic_12( sc_.C_micro1_sl[sl] + sc_.C_micro2_sl[sl]);
194  double const mic_23( sc_.C_micro2_sl[sl] + sc_.C_micro3_sl[sl]);
195 
196  if ( cbm::flt_greater_zero( mic_12))
197  {
198  double const fact_mic_12( sc_.anvf_sl[sl]);
199  double trans_12( (fact_mic_12 * mic_12 - sc_.C_micro2_sl[sl]) * metabolism_rate);
200  if ( cbm::flt_greater_zero( trans_12))
201  {
202  double const trans_max( cbm::bound_min( 0.0, sc_.C_micro1_sl[sl] - MICRO_C_MIN));
203  trans_12 = cbm::bound_max( trans_12, trans_max);
204  sc_.C_micro1_sl[sl] -= trans_12;
205  sc_.C_micro2_sl[sl] += trans_12;
206  }
207  else
208  {
209  double const trans_max( cbm::bound_min( 0.0, sc_.C_micro2_sl[sl] - MICRO_C_MIN));
210  trans_12 = cbm::bound_max( -trans_12, trans_max);
211  sc_.C_micro2_sl[sl] -= trans_12;
212  sc_.C_micro1_sl[sl] += trans_12;
213  }
214  }
215 
216  if ( cbm::flt_greater_zero( mic_23))
217  {
218  double const fact_mic_23( 1.0 - no3_an_sl[sl] / (no3_an_sl[sl] + (NO3_MOLAR_MAX_FE_RED * sc_.h_sl[sl] * M_N_SCALE)));
219  double trans_23( (fact_mic_23 * mic_23 - sc_.C_micro3_sl[sl]) * metabolism_rate);
220  if ( cbm::flt_greater_zero( trans_23))
221  {
222  double const trans_max( cbm::bound_min( 0.0, sc_.C_micro2_sl[sl] - MICRO_C_MIN));
223  trans_23 = cbm::bound_max( trans_23, trans_max);
224  sc_.C_micro2_sl[sl] -= trans_23;
225  sc_.C_micro3_sl[sl] += trans_23;
226  }
227  else
228  {
229  double const trans_max( cbm::bound_min( 0.0, sc_.C_micro3_sl[sl] - MICRO_C_MIN));
230  trans_23 = cbm::bound_max( -trans_23, trans_max);
231  sc_.C_micro3_sl[sl] -= trans_23;
232  sc_.C_micro2_sl[sl] += trans_23;
233  }
234  }
235  }
236  return LDNDC_ERR_OK;
237 }
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◆ MeTrX_microbial_dynamics()

void ldndc::SoilChemistryMeTrX::MeTrX_microbial_dynamics ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_nh3_nh4_equilibrium()

void ldndc::SoilChemistryMeTrX::MeTrX_nh3_nh4_equilibrium ( )
private
Parameters
[in]None
[out]None
Returns
void

References MeTrX_get_ph_wl().

Referenced by solve().

33 {
34  if ( have_water_table)
35  {
36  double ph( MeTrX_get_ph_wl());
37  for ( size_t wl = 0; wl < sb_.surfacebulk_layer_cnt(); wl++)
38  {
39  double const k_a( pow( 10.0,(-2728.3 / (mc_temp_sl[0] + cbm::D_IN_K) - 0.094219))); // Sadeghi et al. (1988) (for 5 < ph < 10)
40 
41  double const n_tot( sb_.nh4_sbl[wl] + sb_.nh3_sbl[wl]);
42  double const frac_nh3( cbm::bound_max( 1.0 / (1.0 + (pow(10.0, - ph) / k_a)), 0.99));
43 
44  double const delta_nh3( frac_nh3 * n_tot - sb_.nh3_sbl[wl]);
45  if( cbm::flt_greater( delta_nh3, 0.0))
46  {
47  sb_.nh3_sbl[wl] += delta_nh3;
48  sb_.nh4_sbl[wl] = cbm::bound_min( 0.0, sb_.nh4_sbl[wl] - delta_nh3);
49  accumulated_n_nh4_nh3_conversion_sbl[wl] += delta_nh3;
50  }
51  else if( cbm::flt_less( delta_nh3, 0.0))
52  {
53  sb_.nh3_sbl[wl] = cbm::bound_min( 0.0, sb_.nh3_sbl[wl] + delta_nh3);
54  sb_.nh4_sbl[wl] -= delta_nh3;
55  accumulated_n_nh3_nh4_conversion_sbl[wl] -= delta_nh3;
56  }
57  }
58  }
59 
60  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
61  {
62  double const k_a( pow( 10.0, -2728.3 / (mc_temp_sl[sl] + cbm::D_IN_K) - 0.094219));
63  double const nh4_tot( nh4_ae_sl[sl] + nh4_an_sl[sl]);
64  double const n_tot( nh4_tot + sc_.nh3_liq_sl[sl]);
65  double const frac_nh3( cbm::bound_max( 1.0 / (1.0 + (pow(10.0, - sc_.ph_sl[sl]) / k_a)), 0.99));
66 
67  double const delta_nh3( frac_nh3 * n_tot - sc_.nh3_liq_sl[sl]);
68  if ( cbm::flt_greater( delta_nh3, 0.0))
69  {
70  sc_.nh3_liq_sl[sl] += delta_nh3;
71  double const delta_nh4_ae( nh4_ae_sl[sl] / nh4_tot * delta_nh3);
72  double const delta_nh4_an( delta_nh3 - delta_nh4_ae);
73  nh4_ae_sl[sl] = cbm::bound_min( 0.0, nh4_ae_sl[sl] - delta_nh4_ae);
74  nh4_an_sl[sl] = cbm::bound_min( 0.0, nh4_an_sl[sl] - delta_nh4_an);
75  accumulated_n_nh4_nh3_conversion_sl[sl] += delta_nh3;
76  }
77  else if ( cbm::flt_less( delta_nh3, 0.0))
78  {
79  sc_.nh3_liq_sl[sl] = cbm::bound_min( 0.0, sc_.nh3_liq_sl[sl] + delta_nh3);
80  nh4_ae_sl[sl] -= delta_nh3 * (1.0 - sc_.anvf_sl[sl]);
81  nh4_an_sl[sl] -= delta_nh3 * sc_.anvf_sl[sl];
82  accumulated_n_nh3_nh4_conversion_sl[sl] -= delta_nh3;
83  }
84  }
85 }
ldndc::SoilChemistryMeTrX::MeTrX_get_ph_wl
double MeTrX_get_ph_wl()
Definition: soilchemistry-metrx-physics-chemistry.cpp:524
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◆ MeTrX_nitrification()

void ldndc::SoilChemistryMeTrX::MeTrX_nitrification ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_nitrogen_fertilizer_release()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_nitrogen_fertilizer_release ( )
private

Transforms nitrogen from slow release nitrogen fertilizer to nh4.

Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

908 {
909  double const coated_nh4_sbl_sum( sb_.coated_nh4_sbl.sum());
910  double const coated_nh4_sl_sum( sc_.coated_nh4_sl.sum());
911  double const coated_nh4_sum( coated_nh4_sbl_sum + coated_nh4_sl_sum);
912  if ( !cbm::flt_greater_zero( coated_nh4_sum))
913  { return LDNDC_ERR_OK; }
914 
915  if ( cbm::flt_greater_zero( coated_nh4_sbl_sum))
916  {
917  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
918  {
919  crnf_.update_crnf( 1.0, mc_temp_sl[0], FTS_TOT_, sb_.nh4_sbl[sbl] / coated_nh4_sum);
920  }
921  }
922 
923  if ( cbm::flt_greater_zero( coated_nh4_sl_sum))
924  {
925  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
926  {
927  crnf_.update_crnf( MeTrX_get_wfps( sl), mc_temp_sl[sl], FTS_TOT_, sc_.coated_nh4_sl[sl] / coated_nh4_sum);
928  }
929  }
930 
931  double coated_nh4_release( crnf_.get_crnf_release( coated_nh4_sum));
932  if ( !cbm::flt_greater_zero( coated_nh4_release))
933  { return LDNDC_ERR_OK; }
934 
935  double const scale( coated_nh4_release / coated_nh4_sum);
936 
937  if ( cbm::flt_greater( scale, 0.99))
938  {
939  if ( cbm::flt_greater_zero( coated_nh4_sbl_sum))
940  {
941  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
942  {
943  sb_.nh4_sbl[sbl] += sb_.coated_nh4_sbl[sbl];
944  sb_.coated_nh4_sbl[sbl] = 0.0;
945  }
946  }
947 
948  if ( cbm::flt_greater_zero( coated_nh4_sl_sum))
949  {
950  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
951  {
952  nh4_ae_sl[sl] += sc_.coated_nh4_sl[sl] * (1.0 - sc_.anvf_sl[sl]);
953  nh4_an_sl[sl] += sc_.coated_nh4_sl[sl] * sc_.anvf_sl[sl];
954  sc_.coated_nh4_sl[sl] = 0.0;
955  }
956  }
957  }
958  else
959  {
960  if ( cbm::flt_greater_zero( coated_nh4_sbl_sum))
961  {
962  for (size_t sbl = 0; sbl < sb_.surfacebulk_layer_cnt(); ++sbl)
963  {
964  if ( cbm::flt_greater_zero( sb_.coated_nh4_sbl[sbl]))
965  {
966  double const n_transform( scale * sb_.coated_nh4_sbl[sbl]);
967  sb_.coated_nh4_sbl[sbl] -= n_transform;
968  sb_.nh4_sbl[sbl] += n_transform;
969  }
970  }
971  }
972 
973  if ( cbm::flt_greater_zero( coated_nh4_sl_sum))
974  {
975  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
976  {
977  if ( cbm::flt_greater_zero( sc_.coated_nh4_sl[sl]))
978  {
979  double const n_transform( scale * sc_.coated_nh4_sl[sl]);
980  sc_.coated_nh4_sl[sl] -= n_transform;
981  nh4_ae_sl[sl] += n_transform * (1.0 - sc_.anvf_sl[sl]);
982  nh4_an_sl[sl] += n_transform * sc_.anvf_sl[sl];
983  }
984  }
985  }
986  }
987 
988  return LDNDC_ERR_OK;
989 }
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◆ MeTrX_pertubation()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_pertubation ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_anaerobic_volume().

Referenced by solve().

1353 {
1354  //Pertubation is only calculated once per day since it is a very slow process
1355  if ( lclock()->subday() == 1)
1356  {
1357  size_t sl_max_1( sl_.soil_layer_cnt()-1);
1358  double nmicro1_lowest_sl(n_micro_1_sl[sl_max_1]);
1359  double nmicro2_lowest_sl(n_micro_2_sl[sl_max_1]);
1360  double nmicro3_lowest_sl(n_micro_3_sl[sl_max_1]);
1361  double naorg_lowest_sl(sc_.N_aorg_sl[sl_max_1]);
1362  double nlit1_lowest_sl(sc_.N_lit1_sl[sl_max_1]);
1363  double nlit2_lowest_sl(sc_.N_lit2_sl[sl_max_1]);
1364  double nlit3_lowest_sl(sc_.N_lit3_sl[sl_max_1]);
1365  double nhum1_lowest_sl(n_humus_1_sl[sl_max_1]);
1366  double nhum2_lowest_sl(n_humus_2_sl[sl_max_1]);
1367  double nhum3_lowest_sl(n_humus_3_sl[sl_max_1]);
1368 
1369  lerr_t rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_micro1_sl, sc_.h_sl, interface_delta_x_soil_sl);
1370  if ( rc){ return rc; }
1371  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, n_micro_1_sl, sc_.h_sl, interface_delta_x_soil_sl);
1372  if ( rc){ return rc; }
1373 
1374  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_micro2_sl, sc_.h_sl, interface_delta_x_soil_sl);
1375  if ( rc){ return rc; }
1376  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, n_micro_2_sl, sc_.h_sl, interface_delta_x_soil_sl);
1377  if ( rc){ return rc; }
1378 
1379  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_micro3_sl, sc_.h_sl, interface_delta_x_soil_sl);
1380  if ( rc){ return rc; }
1381  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, n_micro_3_sl, sc_.h_sl, interface_delta_x_soil_sl);
1382  if ( rc){ return rc; }
1383 
1384  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_aorg_sl, sc_.h_sl, interface_delta_x_soil_sl);
1385  if ( rc){ return rc; }
1386  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.N_aorg_sl, sc_.h_sl, interface_delta_x_soil_sl);
1387  if ( rc){ return rc; }
1388 
1389  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_lit1_sl, sc_.h_sl, interface_delta_x_soil_sl);
1390  if ( rc){ return rc; }
1391  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.N_lit1_sl, sc_.h_sl, interface_delta_x_soil_sl);
1392  if ( rc){ return rc; }
1393 
1394  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_lit2_sl, sc_.h_sl, interface_delta_x_soil_sl);
1395  if ( rc){ return rc; }
1396  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.N_lit2_sl, sc_.h_sl, interface_delta_x_soil_sl);
1397  if ( rc){ return rc; }
1398 
1399  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.C_lit3_sl, sc_.h_sl, interface_delta_x_soil_sl);
1400  if ( rc){ return rc; }
1401  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, sc_.N_lit3_sl, sc_.h_sl, interface_delta_x_soil_sl);
1402  if ( rc){ return rc; }
1403 
1404  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, c_humus_1_sl, sc_.h_sl, interface_delta_x_soil_sl);
1405  if ( rc){ return rc; }
1406  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, n_humus_1_sl, sc_.h_sl, interface_delta_x_soil_sl);
1407  if ( rc){ return rc; }
1408 
1409  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, c_humus_2_sl, sc_.h_sl, interface_delta_x_soil_sl);
1410  if ( rc){ return rc; }
1411  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, n_humus_2_sl, sc_.h_sl, interface_delta_x_soil_sl);
1412  if ( rc){ return rc; }
1413 
1414  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, c_humus_3_sl, sc_.h_sl, interface_delta_x_soil_sl);
1415  if ( rc){ return rc; }
1416  rc = transport_.pertubation(1.0, D_eff_dailyturbation_sl, n_humus_3_sl, sc_.h_sl, interface_delta_x_soil_sl);
1417  if ( rc){ return rc; }
1418 
1419  if ( output_writer_.write_fluxes())
1420  {
1421  /* nmicro */
1422  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, n_micro_1_sl, nmicro1_lowest_sl, communicate_sl);
1423  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1424  {
1425  accumulated_n_micro_perturbation_sl[sl] += communicate_sl[sl];
1426  }
1427  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, n_micro_2_sl, nmicro2_lowest_sl, communicate_sl);
1428  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1429  {
1430  accumulated_n_micro_perturbation_sl[sl] += communicate_sl[sl];
1431  }
1432  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, n_micro_3_sl, nmicro3_lowest_sl, communicate_sl);
1433  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1434  {
1435  accumulated_n_micro_perturbation_sl[sl] += communicate_sl[sl];
1436  }
1437 
1438  /* naorg */
1439  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, sc_.N_aorg_sl, naorg_lowest_sl, communicate_sl);
1440  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1441  {
1442  accumulated_n_aorg_perturbation_sl[sl] += communicate_sl[sl];
1443  }
1444 
1445  /*litter*/
1446  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, sc_.N_lit1_sl, nlit1_lowest_sl, communicate_sl);
1447  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1448  {
1449  accumulated_n_litter_perturbation_sl[sl] += communicate_sl[sl];
1450  }
1451  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, sc_.N_lit2_sl, nlit2_lowest_sl, communicate_sl);
1452  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1453  {
1454  accumulated_n_litter_perturbation_sl[sl] += communicate_sl[sl];
1455  }
1456  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, sc_.N_lit3_sl, nlit3_lowest_sl, communicate_sl);
1457  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1458  {
1459  accumulated_n_litter_perturbation_sl[sl] += communicate_sl[sl];
1460  }
1461 
1462  /*humus*/
1463  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, n_humus_1_sl, nhum1_lowest_sl, communicate_sl);
1464  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1465  {
1466  accumulated_n_humus_1_perturbation_sl[sl] += communicate_sl[sl];
1467  }
1468  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, n_humus_2_sl, nhum2_lowest_sl, communicate_sl);
1469  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1470  {
1471  accumulated_n_humus_2_perturbation_sl[sl] += communicate_sl[sl];
1472  }
1473  transport_.calculate_soil_perturbation_fluxes( sl_.soil_layer_cnt(), 1.0, sc_.h_sl, interface_delta_x_soil_sl, D_eff_dailyturbation_sl, n_humus_3_sl, nhum3_lowest_sl, communicate_sl);
1474  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
1475  {
1476  accumulated_n_humus_3_perturbation_sl[sl] += communicate_sl[sl];
1477  }
1478  }
1479  }
1480  return LDNDC_ERR_OK;
1481 }
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◆ MeTrX_pH_calculation()

void ldndc::SoilChemistryMeTrX::MeTrX_pH_calculation ( )
private
Parameters
[in]None
[out]None
Returns
void

References MeTrX_get_ph_sl().

Referenced by solve().

539 {
540  for ( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
541  {
542  sc_.ph_sl[sl] = MeTrX_get_ph_sl( sl);
543  }
544 }
ldndc::SoilChemistryMeTrX::MeTrX_get_ph_sl
double MeTrX_get_ph_sl(size_t)
Returns dynamic pH-value of given soil layer.
Definition: soilchemistry-metrx-physics-chemistry.cpp:516
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◆ MeTrX_physics()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_physics ( )
private
Parameters
[in]None
[out]None
Returns
error code

References ldndc::d_eff_air_a(), ldndc::d_eff_air_millington_and_quirk_1961(), and TNORM.

Referenced by solve().

156 {
157  /*****************************/
158  /* Water-, Ice-, Air-Content */
159  /*****************************/
160 
161  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
162  {
163  double const v_ice_old( v_ice_sl[sl]);
164  double const v_pores( sc_.h_sl[sl] * sc_.poro_sl[sl]);
165  v_water_sl[sl] = cbm::bound_min( 0.01 * v_pores, wc_.wc_sl[sl] / cbm::DWAT * sc_.h_sl[sl]);
166  v_ice_sl[sl] = cbm::bound_min( 0.0, wc_.ice_sl[sl] / cbm::DICE * sc_.h_sl[sl]);
167  v_air_sl[sl] = cbm::bound_min( 0.05 * v_pores, v_pores - v_water_sl[sl] - v_ice_sl[sl]);
168 
169  pore_connectivity_sl[sl] = cbm::bound(
170  0.001,
171  1.0 - exp( -sipar_.METRX_F_CONNECTIVITY_2() *
172  ((v_air_sl[sl] / sc_.h_sl[sl]) - sipar_.METRX_F_CONNECTIVITY_1())),
173  0.999);
174 
175  if ( have_freeze_thaw)
176  {
177  if ( cbm::flt_greater( v_ice_sl[sl], v_ice_old))
178  {
179  double const freeze_fraction( (v_ice_sl[sl] - v_ice_old) / v_ice_sl[sl]);
180 
181  double const delta_doc( freeze_fraction * (sc_.doc_sl[sl] + sc_.an_doc_sl[sl]));
182  doc_ice_sl[sl] += delta_doc;
183  sc_.doc_sl[sl] *= (1.0 - freeze_fraction);
184  sc_.an_doc_sl[sl] *= (1.0 - freeze_fraction);
185 
186  double const delta_acetate( freeze_fraction * (ae_acetate_sl[sl] + an_acetate_sl[sl]));
187  acetate_ice_sl[sl] += delta_acetate;
188  ae_acetate_sl[sl] *= (1.0 - freeze_fraction);
189  an_acetate_sl[sl] *= (1.0 - freeze_fraction);
190 
191  double const delta_no3( freeze_fraction * (no3_ae_sl[sl] + no3_an_sl[sl]));
192  no3_ice_sl[sl] += delta_no3;
193  no3_ae_sl[sl] *= (1.0 - freeze_fraction);
194  no3_an_sl[sl] *= (1.0 - freeze_fraction);
195 
196  double const delta_nh4( freeze_fraction * (nh4_ae_sl[sl] + nh4_an_sl[sl]));
197  nh4_ice_sl[sl] += delta_nh4;
198  nh4_ae_sl[sl] *= (1.0 - freeze_fraction);
199  nh4_an_sl[sl] *= (1.0 - freeze_fraction);
200 
201  double const delta_don( freeze_fraction * (don_ae_sl[sl] + don_an_sl[sl]));
202  don_ice_sl[sl] += delta_don;
203  don_ae_sl[sl] *= (1.0 - freeze_fraction);
204  don_an_sl[sl] *= (1.0 - freeze_fraction);
205  }
206  else if ( cbm::flt_less( v_ice_sl[sl], v_ice_old))
207  {
208  double const melt_fraction( (v_ice_old > 0.0)? (v_ice_old - v_ice_sl[sl]) / v_ice_old : 1.0);
209 
210  double const delta_doc( melt_fraction * doc_ice_sl[sl]);
211  sc_.doc_sl[sl] += delta_doc * (1.0 - sc_.anvf_sl[sl]);
212  sc_.an_doc_sl[sl] += delta_doc * sc_.anvf_sl[sl];
213  doc_ice_sl[sl] *= (1.0 - melt_fraction);
214 
215  double const delta_acetate( melt_fraction * acetate_ice_sl[sl]);
216  ae_acetate_sl[sl] += delta_acetate * (1.0 - sc_.anvf_sl[sl]);
217  an_acetate_sl[sl] += delta_acetate * sc_.anvf_sl[sl];
218  acetate_ice_sl[sl] *= (1.0 - melt_fraction);
219 
220  double const delta_no3( melt_fraction * no3_ice_sl[sl]);
221  no3_ae_sl[sl] += delta_no3 * (1.0 - sc_.anvf_sl[sl]);
222  no3_an_sl[sl] += delta_no3 * sc_.anvf_sl[sl];
223  no3_ice_sl[sl] *= (1.0 - melt_fraction);
224 
225  double const delta_nh4( melt_fraction * nh4_ice_sl[sl]);
226  nh4_ae_sl[sl] += delta_nh4 * (1.0 - sc_.anvf_sl[sl]);
227  nh4_an_sl[sl] += delta_nh4 * sc_.anvf_sl[sl];
228  nh4_ice_sl[sl] *= (1.0 - melt_fraction);
229 
230  double const delta_don( melt_fraction * don_ice_sl[sl]);
231  don_ae_sl[sl] += delta_don * (1.0 - sc_.anvf_sl[sl]);
232  don_an_sl[sl] += delta_don * sc_.anvf_sl[sl];
233  don_ice_sl[sl] *= (1.0 - melt_fraction);
234  }
235  }
236  }
237 
238  size_t sl_max( sl_.soil_layer_cnt()-1);
239  for (size_t sl = 0; sl < sl_max; ++sl)
240  {
241  interface_air_sl[sl] = cbm::harmonic_mean2( v_air_sl[sl]/sc_.h_sl[sl], v_air_sl[sl+1]/sc_.h_sl[sl+1]);
242  interface_delta_x_air_sl[sl] = interface_air_sl[sl] / delta_x[sl];
243  interface_delta_x_water_sl[sl] = cbm::harmonic_mean2( v_water_sl[sl]/sc_.h_sl[sl], v_water_sl[sl+1]/sc_.h_sl[sl+1]) / delta_x[sl];
244  interface_delta_x_soil_sl[sl] = 1.0;
245  }
246  interface_air_sl[sl_max] = v_air_sl[sl_max]/sc_.h_sl[sl_max];
247  interface_delta_x_air_sl[sl_max] = interface_air_sl[sl_max] / delta_x[sl_max];
248  interface_delta_x_water_sl[sl_max] = v_water_sl[sl_max]/sc_.h_sl[sl_max] / delta_x[sl_max];
249  interface_delta_x_soil_sl[sl_max] = 1.0;
250 
251 
252  double interface_delta_x_atm_soil( 0.0);
253  double interface_delta_x_fl_soil( 0.0);
254  double interface_delta_x_sbl_soil( 0.0);
255 
256  if ( have_water_table)
257  {
258  interface_delta_x_sbl_soil = (cbm::harmonic_mean2( 1.0, v_water_sl[0]/sc_.h_sl[0]) / cbm::arithmetic_mean2( h_wl, sc_.h_sl[0]));
259  }
260  else
261  {
262  /* Set atmospheric Dirichlet boundary condition at ground level */
263  interface_delta_x_atm_soil = (cbm::harmonic_mean2( 1.0, v_air_sl[0]/sc_.h_sl[0]) / (0.5 * sc_.h_sl[0]));
264  interface_delta_x_fl_soil = (cbm::harmonic_mean2( 1.0, v_air_sl[0]/sc_.h_sl[0]) / cbm::arithmetic_mean2( ph_.h_fl[0], sc_.h_sl[0]));
265  }
266 
267 
268 
269  /************************************/
270  /* Effective Diffusion Coefficients */
271  /************************************/
272 
273  /* Plant mediated diffusion */
274 
275  for ( PlantIterator vt = this->m_veg->begin(); vt != this->m_veg->end(); ++vt)
276  {
277  MoBiLE_Plant *p = *vt;
278  if ( cbm::flt_greater_zero( p->root_tc))
279  {
280  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
281  {
282  D_eff_plant_sl[sl] = (p->root_tc * p->fFrt_sl[sl]);
283  }
284  have_plant_diffusion = true;
285  }
286  else
287  {
288  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
289  {
290  D_eff_plant_sl[sl] = 0.0;
291  }
292  have_plant_diffusion = false;
293  }
294  }
295 
296 
297  /* Soil diffusion */
298 
299  /* Effective diffusion coefficients relates to the tortuosity of the soil matrix.
300  * Formular is taken from Lai, S.H., J.M. Tiedje, and A.E. Erickson. 1976.
301  * In situ measurement of gas diffusion coefficient in soils, Soil Sci. Soc. Am. J., 40:3–6
302  * tortuosity = theta^(7/3)
303  * theta refers to soil gas content: volume_gas / volume_soil
304  *
305  * Stone content is considered in order to derive characteristic gas content for soil matrix
306  * only, i.e., excluding the stone fraction of the soil. Stone fractions are implicitly incorporated into
307  * the gaseous diffusion by the reduction of the diffusive interface area between soil layers
308  */
309  if ( d_eff_method == "parameter")
310  {
311  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
312  {
313  double const air_content( v_air_sl[sl] / (sc_.h_sl[sl] * (1.0 - sc_.stone_frac_sl[sl])));
314  double const d_eff( d_eff_air_a( 7.0/3.0, air_content)
315  * pow((mc_temp_sl[sl] + cbm::D_IN_K) / TNORM, sipar_.TEXP())) ;
316 
317  /* Empirical reduction of gaseous diffsuion */
318  D_eff_air_sl[sl] = cbm::bound_max( sipar_.METRX_D_EFF_REDUCTION() * d_eff * sc_.till_effect_sl[sl], 1.0);
319  }
320  }
321  else if ( d_eff_method == "millington_and_quirk_1961")
322  {
323  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
324  {
325  double const air_content( v_air_sl[sl] / (sc_.h_sl[sl] * (1.0 - sc_.stone_frac_sl[sl])));
326  double const d_eff( d_eff_air_millington_and_quirk_1961( air_content, sc_.poro_sl[sl])
327  * pow((mc_temp_sl[sl] + cbm::D_IN_K) / TNORM, sipar_.TEXP())) ;
328 
329  /* Empirical reduction of gaseous diffsuion */
330  D_eff_air_sl[sl] = cbm::bound_max( sipar_.METRX_D_EFF_REDUCTION() * d_eff * sc_.till_effect_sl[sl], 1.0);
331  }
332  }
333  else
334  {
335  KLOGERROR("invalid effective diffusion approach: [", d_eff_method,"]");
336  return LDNDC_ERR_FAIL;
337  }
338 
339  if (wc_.surface_ice > 0.01)
340  {
341  D_eff_air_sl[0] *= 0.01 / wc_.surface_ice;
342  }
343  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
344  {
345  /* Preliminary set to any value */
346  D_eff_water_sl[sl] = pow( MeTrX_get_wfps( sl), 2.0);
347 
348  //pertubation / earthworms activity decreases with depth and soil water saturation
349  D_eff_dailyturbation_sl[sl] = std::exp( - sc_.depth_sl[sl] / sipar_.METRX_F_PERTUBATION_EXP())
350  * sipar_.METRX_F_PERTUBATION_MIX() * (1.0 - MeTrX_get_wfps( sl));
351  }
352 
353  /*******************************/
354  /* Update transport properties */
355  /*******************************/
356 
357  transport_.update_diffusion( D_eff_plant_sl, D_eff_air_sl,
358  v_air_sl,
359  soil_gas_advection_sl,
360  interface_delta_x_air_sl,
361  interface_delta_x_atm_soil,
362  interface_delta_x_fl_soil,
363  interface_delta_x_sbl_soil,
364  h_wl,
365  have_water_table);
366  transport_.update_advection( interface_air_sl);
367 
368  double const d_wind_scale( 1.0 + (*mc_wind) / ((*mc_wind) + 5.0) * 2.0);
369  transport_.wind_stimulation = d_wind_scale;
370 
371  for ( std::map< std::string , double>::iterator it = sc_.n_subdivision.begin();
372  it != sc_.n_subdivision.end(); )
373  {
374  it->second -= 0.02 * FTS_TOT_;
375  if ( !cbm::flt_greater_zero( it->second))
376  {
377  sc_.n_subdivision.erase( it++);
378  }
379  else{ ++it; }
380  }
381 
382  return LDNDC_ERR_OK;
383 }
ldndc::SoilChemistryMeTrX::TNORM
static const double TNORM
Definition: soilchemistry-metrx.h:33
ldndc::d_eff_air_millington_and_quirk_1961
double d_eff_air_millington_and_quirk_1961(double const &, double const &)
Returns effective diffusion coefficient after .
Definition: ld_effective_diffusion_coefficient.cpp:40
ldndc::d_eff_air_a
double d_eff_air_a(double const &, double const &)
Returns effective diffusion coefficient depending on gas content.
Definition: ld_effective_diffusion_coefficient.cpp:16
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◆ MeTrX_receive_state()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_receive_state ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_update().

271 {
272  for ( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
273  {
274  if ( cbm::flt_greater_zero( sc_.nh4_sl[sl]))
275  {
276  double const nh4_old( nh4_ae_sl[sl] + nh4_an_sl[sl]);
277  if ( cbm::flt_greater_zero( nh4_old))
278  {
279  nh4_ae_sl[sl] = cbm::bound_min( 0.0, nh4_ae_sl[sl] / nh4_old * sc_.nh4_sl[sl]);
280  nh4_an_sl[sl] = cbm::bound_min( 0.0, sc_.nh4_sl[sl] - nh4_ae_sl[sl]);
281  }
282  else
283  {
284  nh4_ae_sl[sl] = (1.0 - sc_.anvf_sl[sl]) * sc_.nh4_sl[sl];
285  nh4_an_sl[sl] = sc_.anvf_sl[sl] * sc_.nh4_sl[sl];
286  }
287  }
288  else
289  {
290  nh4_ae_sl[sl] = 0.0;
291  nh4_an_sl[sl] = 0.0;
292  }
293 
294  if ( cbm::flt_greater_zero( sc_.don_sl[sl]))
295  {
296  double const don_old( don_ae_sl[sl] + don_an_sl[sl]);
297  if ( cbm::flt_greater_zero( don_old))
298  {
299  don_ae_sl[sl] = cbm::bound_min( 0.0, don_ae_sl[sl] / don_old * sc_.don_sl[sl]);
300  don_an_sl[sl] = cbm::bound_min( 0.0, sc_.don_sl[sl] - don_ae_sl[sl]);
301  }
302  else
303  {
304  don_ae_sl[sl] = (1.0 - sc_.anvf_sl[sl]) * sc_.don_sl[sl];
305  don_an_sl[sl] = sc_.anvf_sl[sl] * sc_.don_sl[sl];
306  }
307  }
308  else
309  {
310  don_ae_sl[sl] = 0.0;
311  don_an_sl[sl] = 0.0;
312  }
313 
314  double no3_tot( sc_.no3_sl[sl] + sc_.an_no3_sl[sl]);
315  if ( cbm::flt_greater_zero( no3_tot))
316  {
317  double const no3_old( no3_ae_sl[sl] + no3_an_sl[sl]);
318  if ( cbm::flt_greater_zero( no3_old))
319  {
320  no3_ae_sl[sl] = cbm::bound_min( 0.0, no3_ae_sl[sl] / no3_old * no3_tot);
321  no3_an_sl[sl] = cbm::bound_min( 0.0, no3_tot - no3_ae_sl[sl]);
322  }
323  else
324  {
325  no3_ae_sl[sl] = (1.0 - sc_.anvf_sl[sl]) * no3_tot;
326  no3_an_sl[sl] = sc_.anvf_sl[sl] * no3_tot;
327  }
328  }
329  else
330  {
331  no3_ae_sl[sl] = 0.0;
332  no3_an_sl[sl] = 0.0;
333  }
334  }
335 
336  return LDNDC_ERR_OK;
337 }
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◆ MeTrX_reset()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_reset ( )
private
Parameters
[in]None
[out]None
Returns
void

References MeTrX_reset_daily(), and MeTrX_reset_subdaily().

Referenced by solve().

37 {
38  co2_auto_sl = 0.0;
39  co2_hetero_sl = 0.0;
40 
41  if ( timemode_ == TMODE_SUBDAILY)
42  {
43  if ( lclock()->is_position( TMODE_PRE_DAILY))
44  {
45  MeTrX_reset_subdaily();
46  MeTrX_reset_daily();
47  }
48  }
49  else
50  {
51  MeTrX_reset_subdaily();
52  MeTrX_reset_daily();
53  }
54 
55  return LDNDC_ERR_OK;
56 }
ldndc::SoilChemistryMeTrX::MeTrX_reset_subdaily
lerr_t MeTrX_reset_subdaily()
Definition: soilchemistry-metrx-reset.cpp:64
ldndc::SoilChemistryMeTrX::MeTrX_reset_daily
lerr_t MeTrX_reset_daily()
Definition: soilchemistry-metrx-reset.cpp:113
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◆ MeTrX_reset_daily()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_reset_daily ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by MeTrX_reset().

114 {
115  /* Soil layer variables */
116  for (size_t sl = 0; sl < sl_.soil_layer_cnt(); sl++)
117  {
118  plant_o2_consumption_sl[sl] = 0.0;
119 
120  day_nitrify_n2o_sl[sl] = 0.0;
121  day_nit_no2_no3_sl[sl] = 0.0;
122 
123  day_acetate_cons_fe3_sl[sl] = 0.0;
124  day_h2_c_eq_cons_fe3_sl[sl] = 0.0;
125  day_fe2_oxidation_sl[sl] = 0.0;
126 
127  day_acetate_prod_sl[sl] = 0.0;
128 
129  day_ch4_oxidation_sl[sl] = 0.0;
130 
131  day_h2_c_eq_prod_sl[sl] = 0.0;
132  day_ch4_production_acetate_sl[sl] = 0.0;
133  day_ch4_production_hydrogen_sl[sl] = 0.0;
134 
135  day_doc_prod_sl[sl] = 0.0;
136  day_denit_factor_c_sl[sl] = 0.0;
137  day_denit_factor_n_sl[sl] = 0.0;
138  }
139 
140  // Groundwater access
141  day_no3_groundwater_access = 0.0;
142 
143  // Mineralisation
144  day_min_n_decomp = 0.0;
145  day_min_n_aorg = 0.0;
146  day_min_n_mic_1 = 0.0;
147  day_min_n_mic_2 = 0.0;
148  day_min_n_mic_3 = 0.0;
149 
150  // Assimilation
151  day_assi_n_mic_1 = 0.0;
152  day_assi_n_mic_2 = 0.0;
153  day_assi_n_mic_3 = 0.0;
154  day_assi_c_mic_1 = 0.0;
155  day_assi_c_mic_2 = 0.0;
156  day_assi_c_mic_3 = 0.0;
157 
158  // Nitrification
159  day_nit_nh4_no2 = 0.0;
160  day_nit_no2_no = 0.0;
161  day_nit_no2_n2o = 0.0;
162  day_nit_no2_no3_sl = 0.0;
163 
164  // Denitrification
165  day_denit_no3_no2 = 0.0;
166  day_denit_no2_no = 0.0;
167  day_denit_no2_n2o = 0.0;
168  day_denit_no2_n2 = 0.0;
169  day_denit_no_n2o = 0.0;
170  day_denit_no_n2 = 0.0;
171  day_denit_n2o_n2 = 0.0;
172  day_chemodenit_no2_no = 0.0;
173 
174  // Respiration / Fermentation / Methanogenesis
175  day_co2_prod_mic_1_growth = 0.0;
176  day_co2_prod_mic_1_maintenance = 0.0;
177  day_co2_prod_mic_2 = 0.0;
178  day_co2_prod_mic_3_acetate_prod = 0.0;
179  day_co2_prod_mic_3_acetate_cons = 0.0;
180  day_co2_prod_ch4_prod = 0.0;
181  day_co2_prod_ch4_cons = 0.0;
182 
183  // Leaching
184  day_leach_o2 = 0.0;
185  day_leach_n2o = 0.0;
186  day_leach_n2 = 0.0;
187  day_leach_no = 0.0;
188  day_leach_nh3 = 0.0;
189  day_leach_urea = 0.0;
190 
191  // litter
192  dC_root_exsudates = 0.0;
193  dC_litter_algae = 0.0;
194 
195  // Decomposition
196  day_decomp_c_lit_1 = 0.0;
197  day_decomp_c_lit_2 = 0.0;
198  day_decomp_c_lit_3 = 0.0;
199  day_decomp_n_lit_1 = 0.0;
200  day_decomp_n_lit_2 = 0.0;
201  day_decomp_n_lit_3 = 0.0;
202  day_decomp_c_hum_1_sl = 0.0;
203  day_decomp_c_hum_2_sl = 0.0;
204  day_decomp_c_hum_3_sl = 0.0;
205  day_decay_c_mic_sl = 0.0;
206  day_decomp_n_hum_1 = 0.0;
207  day_decomp_n_hum_2 = 0.0;
208  day_decomp_n_hum_3 = 0.0;
209 
210  // Humification
211  day_c_humify_doc_hum_1_sl = 0.0;
212  day_c_humify_sol_hum_1_sl = 0.0;
213  day_c_humify_cel_hum_1_sl = 0.0;
214  day_c_humify_lig_hum_1_sl = 0.0;
215  day_c_humify_lig_hum_2_sl = 0.0;
216  day_c_humify_mic_hum_1_sl = 0.0;
217  day_c_humify_mic_hum_2_sl = 0.0;
218  day_c_humify_hum_1_hum_2_sl = 0.0;
219  day_c_humify_hum_2_hum_3_sl = 0.0;
220 
221  // Algae
222  day_n_fix_algae = 0.0;
223  day_c_fix_algae = 0.0;
224 
225  // DOC production
226  day_doc_prod_decomp_litter = 0.0;
227  day_doc_prod_decomp_humus = 0.0;
228  day_doc_prod_decomp_aorg = 0.0;
229 
230  return LDNDC_ERR_OK;
231 }
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◆ MeTrX_reset_subdaily()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_reset_subdaily ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by MeTrX_reset().

65 {
66  for (size_t ts = 0; ts < TOTAL_TIME_STEPS; ts++)
67  {
68  subdaily_co2_bubbling[ts] = 0.0;
69  subdaily_co2_plant[ts] = 0.0;
70  subdaily_co2_soil[ts] = 0.0;
71  subdaily_co2_water[ts] = 0.0;
72  subdaily_co2_leach[ts] = 0.0;
73 
74  subdaily_ch4_bubbling[ts] = 0.0;
75  subdaily_ch4_plant[ts] = 0.0;
76  subdaily_ch4_soil[ts] = 0.0;
77  subdaily_ch4_water[ts] = 0.0;
78  subdaily_ch4_leach[ts] = 0.0;
79  subdaily_ch4_prod[ts] = 0.0;
80  subdaily_ch4_ox[ts] = 0.0;
81  subdaily_acetate_prod[ts] = 0.0;
82  subdaily_doc_prod[ts] = 0.0;
83  subdaily_plant_o2_cons[ts] = 0.0;
84  subdaily_flood_o2_conc[ts] = 0.0;
85  subdaily_algae_o2_prod[ts] = 0.0;
86  subdaily_o2_bubbling[ts] = 0.0;
87  subdaily_o2_plant[ts] = 0.0;
88  subdaily_o2_soil[ts] = 0.0;
89  subdaily_o2_water[ts] = 0.0;
90  subdaily_n2o_bubbling[ts] = 0.0;
91  subdaily_n2o_plant[ts] = 0.0;
92  subdaily_n2o_soil[ts] = 0.0;
93  subdaily_n2o_water[ts] = 0.0;
94  subdaily_no_bubbling[ts] = 0.0;
95  subdaily_no_plant[ts] = 0.0;
96  subdaily_no_soil[ts] = 0.0;
97  subdaily_no_water[ts] = 0.0;
98  subdaily_nh3_bubbling[ts] = 0.0;
99  subdaily_nh3_plant[ts] = 0.0;
100  subdaily_nh3_soil[ts] = 0.0;
101  subdaily_nh3_water[ts] = 0.0;
102  }
103 
104  return LDNDC_ERR_OK;
105 }
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◆ MeTrX_send_state()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_send_state ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_write_rates().

346 {
347  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
348  {
349  sc_.nh4_sl[sl] = nh4_ae_sl[sl] + nh4_an_sl[sl];
350  sc_.don_sl[sl] = don_ae_sl[sl] + don_an_sl[sl];
351  sc_.no3_sl[sl] = no3_ae_sl[sl] + no3_an_sl[sl];
352  sc_.an_no3_sl[sl] = 0.0;
353  }
354 
355  return LDNDC_ERR_OK;
356 }
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◆ MeTrX_soil_organic_matter_turnover()

void ldndc::SoilChemistryMeTrX::MeTrX_soil_organic_matter_turnover ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

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◆ MeTrX_spinup()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_spinup ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

69 {
70  if ( spinup_.execute_spinup( lclock()))
71  {
72  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
73  {
74  accumulated_n_litter_spinup_sl[sl] -= sc_.n_wood_sl[sl];
75  }
76 
77  /* WOOD */
78  double c_wood( sc_.c_wood);
79  double n_wood( sc_.n_wood);
80  if ( cbm::flt_greater_zero( spinup_.exit_wood) &&
81  cbm::flt_equal_zero( (spinup_.executed_months_+1) % 12))
82  {
83  double const fraction( 0.5);
84  double const c_wood_temp( cbm::bound( 0.5, spinup_.enter_wood / spinup_.exit_wood, 1.5) * sc_.c_wood);
85  sc_.c_wood = c_wood_temp * fraction + c_wood * (1.0 - fraction);
86 
87  double const n_demand_wood( cbm::flt_greater_zero( n_wood) ?
88  sc_.c_wood / (c_wood / n_wood)
89  : 0.0);
90  sc_.n_wood = n_demand_wood;
91 
92  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
93  {
94  double c_wood_sl( sc_.c_wood_sl[sl]);
95  double n_wood_sl( sc_.n_wood_sl[sl]);
96 
97  double const c_wood_sl_temp( cbm::bound( 0.5, spinup_.enter_wood / spinup_.exit_wood, 1.5) * sc_.c_wood_sl[sl]);
98  sc_.c_wood_sl[sl] = c_wood_sl_temp * 0.5 + c_wood_sl * 0.5;
99 
100  double const n_demand_wood_sl( cbm::flt_greater_zero( n_wood_sl) ?
101  sc_.c_wood_sl[sl] / (c_wood_sl / n_wood_sl)
102  : 0.0);
103  sc_.n_wood_sl[sl] = n_demand_wood_sl;
104  }
105  }
106 
107  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
108  {
109  accumulated_n_litter_spinup_sl[sl] += sc_.n_wood_sl[sl];
110  }
111 
112  /* HUMUS */
113  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
114  {
115  for ( int i = 0; i < 10; ++i)
116  {
117  double c_hum_1( c_humus_1_sl[sl]);
118  double n_hum_1( n_humus_1_sl[sl]);
119  double c_hum_2( c_humus_2_sl[sl]);
120  double n_hum_2( n_humus_2_sl[sl]);
121  double c_hum_3( c_humus_3_sl[sl]);
122  double n_hum_3( n_humus_3_sl[sl]);
123 
124  double const c_tot( c_hum_1 + c_hum_2 + c_hum_3);
125  double const n_tot( n_hum_1 + n_hum_2 + n_hum_3);
126 
127  int spinup_steps_per_year( 12);
128  double const delta_c_hum_1( c_hum_1 / (c_hum_1 + c_hum_2) * spinup_.decompose_hum_1[sl] / spinup_.decompose_hum_1.sum()
129  * spinup_delta_c / spinup_steps_per_year);
130  double const delta_c_hum_2( c_hum_2 / (c_hum_1 + c_hum_2) * spinup_.decompose_hum_2[sl] / spinup_.decompose_hum_2.sum()
131  * spinup_delta_c / spinup_steps_per_year);
132 
133  double const c_humus_1_tmp( cbm::bound_min( -1.0e-9, spinup_.humify_c_to_humus_1_sl[sl] - delta_c_hum_1)
134  / (spinup_.decompose_hum_1[sl] + spinup_.humify_humus_1_to_humus_2_sl[sl]));
135 
136  double const c_humus_2_tmp( cbm::bound_min( -1.0e-9, spinup_.humify_c_to_humus_2_sl[sl]
137  + spinup_.humify_humus_1_to_humus_2_sl[sl] * c_humus_1_sl[sl]
138  - delta_c_hum_2)
139  / (spinup_.decompose_hum_2[sl] + spinup_.humify_humus_2_to_humus_3_sl[sl]));
140 
141  //change less with time
142  double const fraction( 0.1);
143 
144  //use upper limit for humus pool 1
145  c_humus_1_sl[sl] = cbm::bound_max( c_humus_1_tmp * fraction + c_hum_1 * (1.0 - fraction), 0.2 * c_tot);
146  c_humus_2_sl[sl] = cbm::bound_max( c_humus_2_tmp * fraction + c_hum_2 * (1.0 - fraction), 0.95 * (c_tot - c_humus_1_sl[sl]));
147  c_humus_3_sl[sl] = c_tot - c_humus_1_sl[sl] -c_humus_2_sl[sl];
148 
149  double const n_demand_humus_1( c_humus_1_sl[sl] / cn_hum_1_sl[sl]);
150  double const n_demand_humus_2( c_humus_2_sl[sl] / cn_hum_2_sl[sl]);
151  double const n_demand_humus_3( c_humus_3_sl[sl] / cn_hum_3_sl[sl]);
152  double const n_demand_tot( n_demand_humus_1 + n_demand_humus_2 + n_demand_humus_3);
153 
154  accumulated_n_humus_1_spinup_sl[sl] -= n_humus_1_sl[sl];
155  accumulated_n_humus_2_spinup_sl[sl] -= n_humus_2_sl[sl];
156  accumulated_n_humus_3_spinup_sl[sl] -= n_humus_3_sl[sl];
157 
158  n_humus_1_sl[sl] = n_demand_humus_1 / n_demand_tot * n_tot;
159  n_humus_2_sl[sl] = n_demand_humus_2 / n_demand_tot * n_tot;
160  n_humus_3_sl[sl] = n_demand_humus_3 / n_demand_tot * n_tot;
161 
162  accumulated_n_humus_1_spinup_sl[sl] += n_humus_1_sl[sl];
163  accumulated_n_humus_2_spinup_sl[sl] += n_humus_2_sl[sl];
164  accumulated_n_humus_3_spinup_sl[sl] += n_humus_3_sl[sl];
165 
166  //adapt only target cn of recalcitrant pools
167  cn_hum_2_sl[sl] = c_humus_2_sl[sl] / n_humus_2_sl[sl];
168  cn_hum_3_sl[sl] = c_humus_3_sl[sl] / n_humus_3_sl[sl];
169  }
170 
171  spinup_.cn_humus_2_temp_sl[sl] += cn_hum_2_sl[sl];
172  spinup_.cn_humus_3_temp_sl[sl] += cn_hum_3_sl[sl];
173 
174  spinup_.c_humus_1_temp_sl[sl] += c_humus_1_sl[sl];
175  spinup_.c_humus_2_temp_sl[sl] += c_humus_2_sl[sl];
176  spinup_.c_humus_3_temp_sl[sl] += c_humus_3_sl[sl];
177  }
178 
179  spinup_.executed_months_ += 1;
180 
181  if ( spinup_.executed_months_ == spinup_.spinup_months())
182  {
183  double const c_hum_tot( c_humus_1_sl.sum() + c_humus_2_sl.sum() + c_humus_3_sl.sum());
184  double const c_hum_1_acc_tot( spinup_.c_humus_1_temp_sl.sum());
185  double const c_hum_2_acc_tot( spinup_.c_humus_2_temp_sl.sum());
186  double const c_hum_3_acc_tot( spinup_.c_humus_3_temp_sl.sum());
187  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
188  {
189  double const c_hum_acc_tot( c_hum_1_acc_tot + c_hum_2_acc_tot + c_hum_3_acc_tot);
190 
191  double const c_hum_1_tot( c_hum_1_acc_tot / c_hum_acc_tot * c_hum_tot);
192  double const c_hum_2_tot( c_hum_2_acc_tot / c_hum_acc_tot * c_hum_tot);
193  double const c_hum_3_tot( c_hum_3_acc_tot / c_hum_acc_tot * c_hum_tot);
194 
195  c_humus_1_sl[sl] = spinup_.c_humus_1_temp_sl[sl] / c_hum_1_acc_tot * c_hum_1_tot;
196  c_humus_2_sl[sl] = spinup_.c_humus_2_temp_sl[sl] / c_hum_2_acc_tot * c_hum_2_tot;
197  c_humus_3_sl[sl] = spinup_.c_humus_3_temp_sl[sl] / c_hum_3_acc_tot * c_hum_3_tot;
198  }
199 
200  double const c_difference( c_hum_tot - (c_humus_1_sl.sum() + c_humus_2_sl.sum() + c_humus_3_sl.sum()));
201  if ( cbm::flt_greater( c_difference, 1.0e-10))
202  {
203  KLOGERROR( name(),": C-leakage during spinup: ", c_difference*cbm::M2_IN_HA, "[kg C ha-1]");
204  }
205 
206  double const n_old_total( n_humus_1_sl.sum() + n_humus_2_sl.sum() + n_humus_3_sl.sum());
207  double n_new_total( 0.0);
208  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
209  {
210  cn_hum_2_sl[sl] = spinup_.cn_humus_2_temp_sl[sl] / spinup_.executed_months_;
211  cn_hum_3_sl[sl] = spinup_.cn_humus_3_temp_sl[sl] / spinup_.executed_months_;
212 
213  n_new_total += c_humus_1_sl[sl] / cn_hum_1_sl[sl];
214  n_new_total += c_humus_2_sl[sl] / cn_hum_2_sl[sl];
215  n_new_total += c_humus_3_sl[sl] / cn_hum_3_sl[sl];
216  }
217 
218  double const scale( n_old_total / n_new_total);
219  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
220  {
221  accumulated_n_humus_1_spinup_sl[sl] -= n_humus_1_sl[sl];
222  accumulated_n_humus_2_spinup_sl[sl] -= n_humus_2_sl[sl];
223  accumulated_n_humus_3_spinup_sl[sl] -= n_humus_3_sl[sl];
224 
225  n_humus_1_sl[sl] = c_humus_1_sl[sl] / cn_hum_1_sl[sl] * scale;
226  n_humus_2_sl[sl] = c_humus_2_sl[sl] / cn_hum_2_sl[sl] * scale;
227  n_humus_3_sl[sl] = c_humus_3_sl[sl] / cn_hum_3_sl[sl] * scale;
228 
229  accumulated_n_humus_1_spinup_sl[sl] += n_humus_1_sl[sl];
230  accumulated_n_humus_2_spinup_sl[sl] += n_humus_2_sl[sl];
231  accumulated_n_humus_3_spinup_sl[sl] += n_humus_3_sl[sl];
232  }
233 
234  double const n_difference( n_old_total - (n_humus_1_sl.sum() + n_humus_2_sl.sum() + n_humus_3_sl.sum()));
235  if ( cbm::flt_greater( c_difference, 1.0e-10))
236  {
237  KLOGERROR( name(),": N-leakage during spinup: ", n_difference*cbm::M2_IN_HA, "[kg N ha-1]");
238  }
239 
240  spinup_.stop_spinup();
241  }
242 
243  spinup_.reset();
244  }
245 
246  return LDNDC_ERR_OK;
247 }
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◆ MeTrX_till()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_till ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by solve().

700 {
701  if ( cbm::flt_greater( sc_.till_effect_sl[0], 1.01))
702  {
703  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
704  {
705  sc_.till_effect_sl[sl] = cbm::bound_min( 1.0, sc_.till_effect_sl[sl] * (1.0 - (sipar_.METRX_TILL_STIMULATION_2() / this->lclock()->time_resolution())));
706  }
707  }
708  else if ( cbm::flt_greater( sc_.till_effect_sl[0], 1.0))
709  {
710  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
711  {
712  sc_.till_effect_sl[sl] = 1.0;
713  }
714  }
715 
716  EventAttributes const * ev_till = NULL;
717  while (( ev_till = this->m_TillEvents.pop()) != NULL)
718  {
719  /***************************/
720  /* tilling depth and layer */
721  /***************************/
722 
723  double till_depth( ev_till->get( "/depth", 0.0));
724  if ( till_depth > 0.5)
725  {
726  KLOGINFO( "tilling depth greater than 0.5m, reset to 0.5m [depth=",till_depth, "m,time=",lclock_ref().to_string(),"]");
727  till_depth = 0.5;
728  }
729 
730  unsigned int till_layer( SL_SURFACE_DISTRIBUTION);
731  if ( cbm::flt_greater_zero( till_depth))
732  {
733  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
734  {
735  if ( sc_.depth_sl[sl] <= till_depth)
736  {
737  sc_.till_effect_sl[sl] = sipar_.METRX_TILL_STIMULATION_1();
738  till_layer = std::max( SL_SURFACE_DISTRIBUTION, sl);
739  }
740  else { break; }
741  }
742  }
743 
744  /**************************************************/
745  /* stubble, root and surface litter incorporation */
746  /**************************************************/
747 
748  sc_.C_lit1_sl[0] += sc_.c_stubble_lit1 + sc_.c_raw_lit_1_sl.sum();
749  sc_.C_lit2_sl[0] += sc_.c_stubble_lit2 + sc_.c_raw_lit_2_sl.sum();
750  sc_.C_lit3_sl[0] += sc_.c_stubble_lit3 + sc_.c_raw_lit_3_sl.sum();
751 
752  sc_.N_lit1_sl[0] += sc_.n_stubble_lit1 + sc_.n_raw_lit_1_sl.sum();
753  sc_.N_lit2_sl[0] += sc_.n_stubble_lit2 + sc_.n_raw_lit_2_sl.sum();
754  sc_.N_lit3_sl[0] += sc_.n_stubble_lit3 + sc_.n_raw_lit_3_sl.sum();
755 
756  accumulated_n_surface_litter_incorporation_via_tilling_sl[0] += sc_.n_stubble_lit1 + sc_.n_stubble_lit2 + sc_.n_stubble_lit3 ;
757  accumulated_n_litter_tilling_sl[0] += sc_.n_raw_lit_1_sl.sum() + sc_.n_raw_lit_2_sl.sum() + sc_.n_raw_lit_3_sl.sum();
758 
759  sc_.c_stubble_lit1 = sc_.c_stubble_lit2 = sc_.c_stubble_lit3 = 0.0;
760  sc_.n_stubble_lit1 = sc_.n_stubble_lit2 = sc_.n_stubble_lit3 = 0.0;
761 
762  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
763  {
764  accumulated_n_litter_tilling_sl[sl] -= sc_.N_lit1_sl[sl] + sc_.N_lit2_sl[sl] + sc_.N_lit3_sl[sl] + sc_.n_raw_lit_1_sl[sl] + sc_.n_raw_lit_2_sl[sl] + sc_.n_raw_lit_3_sl[sl];
765  accumulated_n_aorg_tilling_sl[sl] -= sc_.N_aorg_sl[sl];
766  accumulated_n_humus_1_tilling_sl[sl] -= n_humus_1_sl[sl];
767  accumulated_n_humus_2_tilling_sl[sl] -= n_humus_2_sl[sl];
768  accumulated_n_humus_3_tilling_sl[sl] -= n_humus_3_sl[sl];
769  accumulated_n_no3_tilling_sl[sl] -= no3_ae_sl[sl] + no3_an_sl[sl];
770  accumulated_n_no2_tilling_sl[sl] -= sc_.no2_sl[sl] + sc_.an_no2_sl[sl];
771  accumulated_n_no_tilling_sl[sl] -= no_gas_sl[sl] + no_liq_sl[sl] + an_no_gas_sl[sl] + an_no_liq_sl[sl];
772  accumulated_n_n2o_tilling_sl[sl] -= n2o_gas_sl[sl] + n2o_liq_sl[sl] + an_n2o_gas_sl[sl] + an_n2o_liq_sl[sl];
773  accumulated_n_urea_tilling_sl[sl] -= sc_.urea_sl[sl];
774  accumulated_n_don_tilling_sl[sl] -= don_ae_sl[sl] + don_an_sl[sl];
775  accumulated_n_nh4_tilling_sl[sl] -= nh4_ae_sl[sl] + nh4_an_sl[sl] + sc_.clay_nh4_sl[sl];
776  accumulated_n_nh3_tilling_sl[sl] -= sc_.nh3_gas_sl[sl] + sc_.nh3_liq_sl[sl];
777  accumulated_n_microbes_tilling_sl[sl] -= n_micro_1_sl[sl] + n_micro_2_sl[sl] + n_micro_3_sl[sl];
778  }
779 
780  sc_.c_raw_lit_1_sl = sc_.c_raw_lit_2_sl = sc_.c_raw_lit_3_sl = 0.0;
781  sc_.n_raw_lit_1_sl = sc_.n_raw_lit_2_sl = sc_.n_raw_lit_3_sl = 0.0;
782 
783  /****************************************/
784  /* rearranging soil pools after tilling */
785  /****************************************/
786 
787  lvector_t< double > pool_buf[] =
788  {
789  sc_.fe2_sl, sc_.fe3_sl,
790  sc_.C_lit1_sl, sc_.C_lit2_sl, sc_.C_lit3_sl,
791  sc_.N_lit1_sl, sc_.N_lit2_sl, sc_.N_lit3_sl,
792  sc_.C_aorg_sl, sc_.N_aorg_sl,
793  sc_.C_micro1_sl, sc_.C_micro2_sl, sc_.C_micro3_sl,
794  n_micro_1_sl, n_micro_2_sl, n_micro_3_sl,
795  c_humus_1_sl, c_humus_2_sl, c_humus_3_sl,
796  n_humus_1_sl, n_humus_2_sl, n_humus_3_sl,
797  sc_.doc_sl, sc_.an_doc_sl,
798  ae_acetate_sl, an_acetate_sl,
799  no3_ae_sl, no3_an_sl,
800  sc_.no2_sl, sc_.an_no2_sl,
801  don_ae_sl, don_an_sl,
802  nh4_ae_sl, nh4_an_sl, sc_.clay_nh4_sl,
803  sc_.urea_sl, sc_.nh3_gas_sl, sc_.nh3_liq_sl,
804  no_gas_sl, no_liq_sl, an_no_gas_sl, an_no_liq_sl,
805  n2o_gas_sl, n2o_liq_sl, an_n2o_gas_sl, an_n2o_liq_sl
806  };
807 
808  size_t const pools_cnt( sizeof( pool_buf) / sizeof(lvector_t< double >));
809  for ( size_t k = 0; k < pools_cnt; ++k)
810  {
811  // summing up pool down to tilling depth
812  double pool_sum( pool_buf[k].sum( till_layer) / sc_.depth_sl[till_layer-1]);
813  for ( size_t l = 0; l < till_layer; l++)
814  {
815  pool_buf[k][l] = pool_sum * sc_.h_sl[l];
816  }
817  }
818 
819  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
820  {
821  accumulated_n_litter_tilling_sl[sl] += sc_.N_lit1_sl[sl] + sc_.N_lit2_sl[sl] + sc_.N_lit3_sl[sl] + sc_.n_raw_lit_1_sl[sl] + sc_.n_raw_lit_2_sl[sl] + sc_.n_raw_lit_3_sl[sl];
822  accumulated_n_aorg_tilling_sl[sl] += sc_.N_aorg_sl[sl];
823  accumulated_n_humus_1_tilling_sl[sl] += n_humus_1_sl[sl];
824  accumulated_n_humus_2_tilling_sl[sl] += n_humus_2_sl[sl];
825  accumulated_n_humus_3_tilling_sl[sl] += n_humus_3_sl[sl];
826  accumulated_n_no3_tilling_sl[sl] += no3_ae_sl[sl] + no3_an_sl[sl];
827  accumulated_n_no2_tilling_sl[sl] += sc_.no2_sl[sl] + sc_.an_no2_sl[sl];
828  accumulated_n_no_tilling_sl[sl] += no_gas_sl[sl] + no_liq_sl[sl] + an_no_gas_sl[sl] + an_no_liq_sl[sl];
829  accumulated_n_n2o_tilling_sl[sl] += n2o_gas_sl[sl] + n2o_liq_sl[sl] + an_n2o_gas_sl[sl] + an_n2o_liq_sl[sl];
830  accumulated_n_urea_tilling_sl[sl] += sc_.urea_sl[sl];
831  accumulated_n_don_tilling_sl[sl] += don_ae_sl[sl] + don_an_sl[sl];
832  accumulated_n_nh4_tilling_sl[sl] += nh4_ae_sl[sl] + nh4_an_sl[sl] + sc_.clay_nh4_sl[sl];
833  accumulated_n_nh3_tilling_sl[sl] += sc_.nh3_gas_sl[sl] + sc_.nh3_liq_sl[sl];
834  accumulated_n_microbes_tilling_sl[sl] += n_micro_1_sl[sl] + n_micro_2_sl[sl] + n_micro_3_sl[sl];
835  }
836  }
837 
838  return LDNDC_ERR_OK;
839 }
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◆ MeTrX_update()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_update ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_receive_state(), MeTrX_update_soil_discretization(), ldndc::update_litter_height(), and ldndc::wood_initialization().

Referenced by solve().

64 {
65  lerr_t rc = MeTrX_receive_state();
66  if ( rc)
67  {
68  return LDNDC_ERR_FAIL;
69  }
70 
71  /* vertical discretization */
72  if ( !have_no_litter_height_change)
73  {
74  lerr_t rc_litter = update_litter_height( sl_, wc_, sc_);
75  if ( rc_litter){ return LDNDC_ERR_FAIL; }
76 
77  //lerr_t rc_soil = update_soil_height( sl_, wc_, sc_);
78  //if ( rc_soil){ return LDNDC_ERR_FAIL; }
79 
80  MeTrX_update_soil_discretization();
81  }
82 
83  /* module specific variables from global state */
84  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
85  {
86  /* use liq/gas distribution from previous time step */
87  UPDATE_STATE( no_liq_sl[sl], no_gas_sl[sl], sc_.no_sl[sl]);
88  UPDATE_STATE( an_no_liq_sl[sl], an_no_gas_sl[sl], sc_.an_no_sl[sl]);
89  UPDATE_STATE( n2o_liq_sl[sl], n2o_gas_sl[sl], sc_.n2o_sl[sl]);
90  UPDATE_STATE( an_n2o_liq_sl[sl], an_n2o_gas_sl[sl], sc_.an_n2o_sl[sl]);
91 
92  CHECK_FOR_ZERO( sc_.C_lit1_sl[sl]);
93  CHECK_FOR_ZERO( sc_.C_lit2_sl[sl]);
94  CHECK_FOR_ZERO( sc_.C_lit3_sl[sl]);
95  CHECK_FOR_ZERO( sc_.N_lit1_sl[sl]);
96  CHECK_FOR_ZERO( sc_.N_lit2_sl[sl]);
97  CHECK_FOR_ZERO( sc_.N_lit3_sl[sl]);
98  }
99 
100  /* water table */
101  if ( cbm::flt_greater( wc_.surface_water, 0.01) &&
102  (sb_.surfacebulk_layer_cnt() > 0))
103  {
104  have_water_table = true;
105 
106  // for simplicity of calculations changing watertable
107  // alters heigth of single waterlayer and not number of layers
108  h_wl = (wc_.surface_water / (double)sb_.surfacebulk_layer_cnt());
109  }
110  else if ( !cbm::flt_greater( wc_.surface_ice, 0.0))
111  {
112  have_water_table = false;
113  h_wl = 0.0;
114 
115  double const clear_ch4( sb_.ch4_sbl.sum());
116  sb_.ch4_sbl = 0.0;
117  double const clear_o2( sb_.o2_sbl.sum());
118  sb_.o2_sbl = 0.0;
119  double const clear_nh4( sb_.nh4_sbl.sum());
120  sb_.nh4_sbl = 0.0;
121  double const clear_nh3( sb_.nh3_sbl.sum());
122  sb_.nh3_sbl = 0.0;
123  double const clear_urea( sb_.urea_sbl.sum());
124  sb_.urea_sbl = 0.0;
125  double const clear_no3( sb_.no3_sbl.sum());
126  sb_.no3_sbl = 0.0;
127  double const clear_don( sb_.don_sbl.sum());
128  sb_.don_sbl = 0.0;
129  double const clear_doc( sb_.doc_sbl.sum());
130  sb_.doc_sbl = 0.0;
131  double const clear_co2( sb_.co2_sbl.sum());
132  sb_.co2_sbl = 0.0;
133  double const clear_so4( sb_.so4_sbl.sum());
134  sb_.so4_sbl = 0.0;
135 
136  for( size_t sl = 0; sl <= SL_SURFACE_DISTRIBUTION; ++sl)
137  {
138  ch4_liq_sl[sl] += clear_ch4 * SL_SURFACE_DISTRIBUTION_INVERSE;
139  o2_liq_sl[sl] += clear_o2 * SL_SURFACE_DISTRIBUTION_INVERSE;
140  nh4_ae_sl[sl] += clear_nh4 * SL_SURFACE_DISTRIBUTION_INVERSE;
141  sc_.nh3_liq_sl[sl] += clear_nh3 * SL_SURFACE_DISTRIBUTION_INVERSE;
142  sc_.urea_sl[sl] += clear_urea * SL_SURFACE_DISTRIBUTION_INVERSE;
143  no3_ae_sl[sl] += clear_no3 * SL_SURFACE_DISTRIBUTION_INVERSE;
144  don_ae_sl[sl] += clear_don * SL_SURFACE_DISTRIBUTION_INVERSE;
145  sc_.doc_sl[sl] += clear_doc * SL_SURFACE_DISTRIBUTION_INVERSE;
146  co2_liq_sl[sl] += clear_co2 * SL_SURFACE_DISTRIBUTION_INVERSE;
147  sc_.so4_sl[sl] += clear_so4 * SL_SURFACE_DISTRIBUTION_INVERSE;
148 
149  accumulated_n_nh4_infiltration_phys_sl[sl] += clear_nh4 * SL_SURFACE_DISTRIBUTION_INVERSE;
150  accumulated_n_nh3_infiltration_phys_sl[sl] += clear_nh3 * SL_SURFACE_DISTRIBUTION_INVERSE;
151  accumulated_n_urea_infiltration_phys_sl[sl] += clear_urea * SL_SURFACE_DISTRIBUTION_INVERSE;
152  accumulated_n_no3_infiltration_phys_sl[sl] += clear_no3 * SL_SURFACE_DISTRIBUTION_INVERSE;
153  accumulated_n_don_infiltration_phys_sl[sl] += clear_don * SL_SURFACE_DISTRIBUTION_INVERSE;
154  }
155  }
156 
157  /* water fluxes */
158  infiltration = wc_.accumulated_infiltration - accumulated_infiltration_old;
159  accumulated_infiltration_old = wc_.accumulated_infiltration;
160  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
161  {
162  waterflux_sl[sl] = wc_.accumulated_waterflux_sl[sl] - accumulated_waterflux_old_sl[sl];
163  accumulated_waterflux_old_sl[sl] = wc_.accumulated_waterflux_sl[sl];
164  }
165 
166  /* nitrogen deposition */
167  if ( cbm::flt_greater_zero( wc_.surface_water) || cbm::flt_greater_zero( wc_.surface_ice))
168  {
169  accumulated_n_nh4_throughfall_sbl[0] += ph_.accumulated_nh4_throughfall - accumulated_n_nh4_throughfall_old;
170  accumulated_n_no3_throughfall_sbl[0] += ph_.accumulated_no3_throughfall - accumulated_n_no3_throughfall_old;
171  }
172  else
173  {
174  accumulated_n_nh4_throughfall_sl[0] += ph_.accumulated_nh4_throughfall - accumulated_n_nh4_throughfall_old;
175  accumulated_n_no3_throughfall_sl[0] += ph_.accumulated_no3_throughfall - accumulated_n_no3_throughfall_old;
176  }
177  accumulated_n_nh4_throughfall_old = ph_.accumulated_nh4_throughfall;
178  accumulated_n_no3_throughfall_old = ph_.accumulated_no3_throughfall;
179 
180  /* carbon/nitrogen flux planting */
181  EventAttributes const * ev_plant = NULL;
182  while (( ev_plant = this->m_PlantEvents.pop()) != NULL)
183  {
184  MoBiLE_Plant *p = m_veg->get_plant( ev_plant->get( "/name", "?"));
185  if ( p)
186  {
187  accumulated_n_to_living_plant_and_algae_from_extern_sl[0] += p->total_nitrogen();
188 
189  if ( spinup_.spinup_stage( this->lclock()))
190  {
191  site::input_class_site_t const *s_site( io_kcomm->get_input_class< site::input_class_site_t >());
192  ldndc::wood_initialization(sl_, p, sc_, s_site->soil_use_history());
193  }
194  }
195  }
196 
197  /* carbon/nitrogen flux harvest/cutting */
198  accumulated_n_export_harvest_cutting_grazing += ph_.accumulated_n_export_harvest - accumulated_n_export_harvest_old;
199  accumulated_n_export_harvest_old = ph_.accumulated_n_export_harvest;
200 
201  /* carbon/nitrogen flux litterfall */
202  if ( spinup_.spinup_stage( this->lclock()))
203  {
204  double const delta_c_wood( sc_.accumulated_c_litter_wood_above - accumulated_c_litter_wood_above_old);
205  if ( cbm::flt_greater_zero( delta_c_wood))
206  {
207  spinup_.enter_wood += delta_c_wood;
208  }
209  }
210  accumulated_c_litter_wood_above_old = sc_.accumulated_c_litter_wood_above;
211  accumulated_n_litter_from_plants_above_wood = sc_.accumulated_n_litter_wood_above;
212  accumulated_n_litter_from_plants_above_rawlitter = sc_.accumulated_n_litter_above;
213  accumulated_n_litter_from_plants_above_stubble = sc_.accumulated_n_litter_stubble;
214  for ( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
215  {
216  accumulated_n_litter_from_plants_below_rawlitter_sl[sl] = sc_.accumulated_n_litter_below_sl[sl];
217  accumulated_n_litter_from_plants_below_wood_sl[sl] = sc_.accumulated_n_litter_wood_below_sl[sl];
218  }
219 
220  /* carbon/nitrogen flux root exsudation */
221  double const delta_c_exsudation( sc_.accumulated_c_root_exsudates_sl.sum() -
222  accumulated_c_root_exsudates_old_sl.sum());
223  if ( cbm::flt_greater_zero( delta_c_exsudation))
224  {
225  dC_root_exsudates += delta_c_exsudation;
226  subdaily_doc_prod[subdaily_time_step_] += delta_c_exsudation;
227  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
228  {
229  double const delta_c_exsudation_sl( sc_.accumulated_c_root_exsudates_sl[sl] - accumulated_c_root_exsudates_old_sl[sl]);
230  day_doc_prod_sl[sl] += delta_c_exsudation_sl;
231  accumulated_c_root_exsudates_old_sl[sl] = sc_.accumulated_c_root_exsudates_sl[sl];
232  }
233  }
234 
235  /* litter layer characterization */
236  double bio_coniferous( 0.0);
237  double bio_deciduous( 0.0);
238  for ( PlantIterator vt = this->m_veg->begin(); vt != this->m_veg->end(); ++vt)
239  {
240  MoBiLE_Plant *p( *vt);
241  if ( (*p)->DECIDUOUS())
242  {
243  bio_deciduous += p->aboveground_biomass();
244  }
245  else
246  {
247  bio_coniferous += p->aboveground_biomass();
248  }
249  }
250  double const bio_tot( bio_deciduous + bio_coniferous);
251  if ( cbm::flt_greater_zero( bio_tot))
252  {
253  double const frac_deciduous( bio_deciduous / bio_tot);
254  double const frac_coniferous( 1.0 - frac_deciduous);
255  for (size_t sl = 0; sl <= SL_SURFACE_DISTRIBUTION; ++sl)
256  {
257  litter_type_fact_sl[sl] = (frac_deciduous + sipar_.METRX_KR_REDUCTION_CONIFEROUS() * frac_coniferous);
258  }
259  }
260 
261  return LDNDC_ERR_OK;
262 }
ldndc::update_litter_height
lerr_t update_litter_height(soillayers::input_class_soillayers_t const &, substate_watercycle_t &, substate_soilchemistry_t &)
Detailed description provided here .
Definition: ld_litterheight.cpp:26
ldndc::SoilChemistryMeTrX::MeTrX_update_soil_discretization
lerr_t MeTrX_update_soil_discretization()
Definition: soilchemistry-metrx-reset.cpp:19
ldndc::wood_initialization
lerr_t wood_initialization(soillayers::input_class_soillayers_t const &, MoBiLE_Plant *, substate_soilchemistry_t &, ecosystem_type_e)
Initialization of aboveground and belowground wood debris, derived from existing vegetation.
Definition: ld_wood_initialization.cpp:18
ldndc::SoilChemistryMeTrX::MeTrX_receive_state
lerr_t MeTrX_receive_state()
Definition: soilchemistry-metrx-communicate.cpp:270
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◆ MeTrX_update_soil_discretization()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_update_soil_discretization ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_update().

20 {
21  for( size_t sl = 0; sl < sl_.soil_layer_cnt()-1; ++sl)
22  {
23  delta_x[sl] = cbm::arithmetic_mean2( sc_.h_sl[sl], sc_.h_sl[sl+1]);
24  }
25  delta_x[sl_.soil_layer_cnt()-1] = sc_.h_sl[sl_.soil_layer_cnt()-1];
26 
27  return LDNDC_ERR_OK;
28 }
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◆ MeTrX_urea_hydrolysis()

void ldndc::SoilChemistryMeTrX::MeTrX_urea_hydrolysis ( )
private
Parameters
[in]None
[out]None
Returns
void

Referenced by solve().

858 {
859  if ( have_water_table)
860  {
861  double nh4_prod_sum( 0.0);
862  for (size_t wl = 0; wl < sb_.surfacebulk_layer_cnt(); wl++)
863  {
864  double const fact_t( 0.25 * exp(0.0693 * mc_temp_sl[0]));
865  double const nh4_prod( sb_.urea_sbl[wl]
866  * cbm::bound( 0.0,
867  1.0 - exp( -fact_t * 0.02),
868  0.9));
869  sb_.urea_sbl[wl] -= nh4_prod;
870  sb_.nh4_sbl[wl] += nh4_prod;
871  accumulated_n_urea_nh4_hydrolysis_sbl[0] += nh4_prod;
872  nh4_prod_sum += nh4_prod;
873  }
874  ph_delta_urea_wl = cbm::bound( 0.0, nh4_prod_sum / (sipar_.METRX_KMM_PH_INCREASE_FROM_UREA() * wc_.surface_water), PH_MAX-PH_SURFACE_WATER);
875  }
876 
877  for ( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
878  {
879  if ( cbm::flt_greater_zero( sc_.urea_sl[sl]))
880  {
881  double const fact_t( 0.25 * exp(0.0693 * mc_temp_sl[sl]));
882  double const nh4_prod( sc_.urea_sl[sl]
883  * cbm::bound( 0.0,
884  1.0 - exp( -fact_t * 0.02),
885  0.9));
886 
887  sc_.urea_sl[sl] -= nh4_prod;
888  nh4_ae_sl[sl] += nh4_prod * (1.0 - sc_.anvf_sl[sl]);
889  nh4_an_sl[sl] += nh4_prod * sc_.anvf_sl[sl];
890  accumulated_n_urea_nh4_hydrolysis_sl[sl] += nh4_prod;
891  ph_delta_urea_sl[sl] = cbm::bound( 0.0, nh4_prod / (sipar_.METRX_KMM_PH_INCREASE_FROM_UREA() * sc_.h_sl[sl]), PH_MAX-sc_.phi_sl[sl]);
892  }
893  else
894  {
895  sc_.urea_sl[sl] = 0.0;
896  ph_delta_urea_sl[sl] = 0.0;
897  }
898  }
899 }
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◆ MeTrX_write_output()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_write_output_daily(), MeTrX_write_output_fluxes(), MeTrX_write_output_layer_daily(), MeTrX_write_output_layer_yearly(), MeTrX_write_output_pools(), MeTrX_write_output_subdaily(), and MeTrX_write_output_yearly().

Referenced by solve().

17 {
18  if ( !output_data_ || !this->output_writer_.active())
19  {
20  return LDNDC_ERR_OK;
21  }
22 
23  if ( output_writer_.write_subdaily())
24  {
25  lerr_t rc_out = MeTrX_write_output_subdaily();
26  if ( rc_out){ return LDNDC_ERR_FAIL; }
27  }
28 
29  if ( output_writer_.write_fluxes())
30  {
31  lerr_t rc_out = MeTrX_write_output_fluxes();
32  if ( rc_out){ return LDNDC_ERR_FAIL; }
33  }
34 
35  if ( lclock()->is_position( TMODE_POST_DAILY))
36  {
37  if ( output_writer_.write_pools())
38  {
39  lerr_t rc_out = MeTrX_write_output_pools();
40  if ( rc_out){ return LDNDC_ERR_FAIL; }
41  }
42 
43  if ( output_writer_.write_daily())
44  {
45  lerr_t rc_out = MeTrX_write_output_daily();
46  if ( rc_out){ return LDNDC_ERR_FAIL; }
47  }
48 
49  if ( output_writer_.write_layer_daily())
50  {
51  lerr_t rc_out = MeTrX_write_output_layer_daily();
52  if ( rc_out){ return LDNDC_ERR_FAIL; }
53  }
54  }
55 
56  if ( lclock()->is_position( TMODE_POST_YEARLY))
57  {
58  if ( output_writer_.write_yearly())
59  {
60  lerr_t rc_out = MeTrX_write_output_yearly();
61  if ( rc_out){ return LDNDC_ERR_FAIL; }
62  }
63 
64  if ( output_writer_.write_layer_yearly())
65  {
66  lerr_t rc_out = MeTrX_write_output_layer_yearly();
67  if ( rc_out){ return LDNDC_ERR_FAIL; }
68  }
69  }
70 
71  return LDNDC_ERR_OK;
72 }
ldndc::SoilChemistryMeTrX::MeTrX_write_output_layer_yearly
lerr_t MeTrX_write_output_layer_yearly()
Definition: soilchemistry-metrx-output.cpp:602
ldndc::SoilChemistryMeTrX::MeTrX_write_output_subdaily
lerr_t MeTrX_write_output_subdaily()
Definition: soilchemistry-metrx-output.cpp:944
ldndc::SoilChemistryMeTrX::MeTrX_write_output_pools
lerr_t MeTrX_write_output_pools()
Definition: soilchemistry-metrx-output.cpp:629
ldndc::SoilChemistryMeTrX::MeTrX_write_output_daily
lerr_t MeTrX_write_output_daily()
Definition: soilchemistry-metrx-output.cpp:76
ldndc::SoilChemistryMeTrX::MeTrX_write_output_fluxes
lerr_t MeTrX_write_output_fluxes()
Definition: soilchemistry-metrx-output.cpp:698
ldndc::SoilChemistryMeTrX::MeTrX_write_output_layer_daily
lerr_t MeTrX_write_output_layer_daily()
Definition: soilchemistry-metrx-output.cpp:435
ldndc::SoilChemistryMeTrX::MeTrX_write_output_yearly
lerr_t MeTrX_write_output_yearly()
Definition: soilchemistry-metrx-output.cpp:391
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◆ MeTrX_write_output_daily()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_daily ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_get_ph_wl().

Referenced by MeTrX_write_output().

77 {
78 #define METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT(__val__) LDNDC_OUTPUT_SET_COLUMN_((__val__),=,output_data_,1)
79  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
80 
81  double const clit1( sc_.C_lit1_sl.sum() + sc_.c_raw_lit_1_sl.sum());
82  double const clit2( sc_.C_lit2_sl.sum() + sc_.c_raw_lit_2_sl.sum());
83  double const clit3( sc_.C_lit3_sl.sum() + sc_.c_raw_lit_3_sl.sum());
84  double const nlit1( sc_.N_lit1_sl.sum() + sc_.n_raw_lit_1_sl.sum());
85  double const nlit2( sc_.N_lit2_sl.sum() + sc_.n_raw_lit_2_sl.sum());
86  double const nlit3( sc_.N_lit3_sl.sum() + sc_.n_raw_lit_3_sl.sum());
87 
88  double const cmic1( sc_.C_micro1_sl.sum());
89  double const cmic2( sc_.C_micro2_sl.sum());
90  double const cmic3( sc_.C_micro3_sl.sum());
91  double const nmic1( n_micro_1_sl.sum());
92  double const nmic2( n_micro_2_sl.sum());
93  double const nmic3( n_micro_3_sl.sum());
94 
95  double const cstub( sc_.c_stubble_lit1+sc_.c_stubble_lit2+sc_.c_stubble_lit3);
96  double const nstub( sc_.n_stubble_lit1+sc_.n_stubble_lit2+sc_.n_stubble_lit3);
97 
98  double const chum1( c_humus_1_sl.sum());
99  double const chum2( c_humus_2_sl.sum());
100  double const chum3( c_humus_3_sl.sum());
101  double const nhum1( n_humus_1_sl.sum());
102  double const nhum2( n_humus_2_sl.sum());
103  double const nhum3( n_humus_3_sl.sum());
104 
105  double const caorg( sc_.C_aorg_sl.sum());
106  double const naorg( sc_.N_aorg_sl.sum());
107 
108  double const cwood( sc_.c_wood_sl.sum()+sc_.c_wood);
109  double const nwood( sc_.n_wood_sl.sum()+sc_.n_wood);
110 
111  double const n_algae_tot( n_algae + n_dead_algae);
112  double const don_sum( don_ae_sl.sum()+don_an_sl.sum()+sb_.don_sbl.sum());
113  double const nh4_sum( nh4_ae_sl.sum()+nh4_an_sl.sum()+sb_.nh4_sbl.sum());
114  double const nh4_clay_sum( sc_.clay_nh4_sl.sum());
115  double const coated_nh4_sum( sc_.coated_nh4_sl.sum());
116  double const urea_sum( sc_.urea_sl.sum()+sb_.urea_sbl.sum());
117  double const no2_sum( sc_.no2_sl.sum());
118  double const an_no2_sum( sc_.an_no2_sl.sum());
119  double const no3_sum( no3_ae_sl.sum());
120  double const an_no3_sum( no3_an_sl.sum()+sb_.no3_sbl.sum());
121  double const n2o_sum( n2o_gas_sl.sum()+n2o_liq_sl.sum());
122  double const an_n2o_sum( an_n2o_gas_sl.sum()+an_n2o_liq_sl.sum());
123  double const no_sum( no_gas_sl.sum()+no_liq_sl.sum());
124  double const an_no_sum( an_no_gas_sl.sum()+an_no_liq_sl.sum());
125  double const nh3_gas_sum( sc_.nh3_gas_sl.sum());
126  double const nh3_liq_sum( sc_.nh3_liq_sl.sum()+sb_.nh3_sbl.sum());
127 
128  double const n_sbl( sb_.don_sbl.sum() + sb_.nh4_sbl.sum()
129  + sb_.urea_sbl.sum() + sb_.no3_sbl.sum() + sb_.nh3_sbl.sum());
130  double const nsol( nh4_sum + nh4_clay_sum + don_sum
131  + nh3_gas_sum + nh3_liq_sum + urea_sum
132  + no3_sum + an_no3_sum + no2_sum + an_no2_sum
133  + n2o_sum + an_n2o_sum + no_sum + an_no_sum);
134 
135  double const c_algae_tot( c_algae + c_dead_algae);
136  double const doc_sum( sc_.doc_sl.sum());
137  double const an_doc_sum( sc_.an_doc_sl.sum());
138  double const acetate_sum( ae_acetate_sl.sum() + an_acetate_sl.sum());
139  double const ch4_gas_sum( ch4_gas_sl.sum());
140  double const ch4_liq_sum( ch4_liq_sl.sum());
141 
142  double const csol( doc_sum + an_doc_sum + acetate_sum + ch4_gas_sum + ch4_liq_sum);
143 
144  double soc20( 0.0);
145  double soc40( 0.0);
146  double totn20( 0.0);
147  double totn40( 0.0);
148  double soilmass20( 0.0);
149  double soilmass40( 0.0);
150  double anvf_avg( 0.0);
151 #ifdef METRX_ANVF_TYPES
152  double anvf_avg_pnet( 0.0);
153  double anvf_avg_dndc_can( 0.0);
154  double anvf_avg_nloss( 0.0);
155 #endif
156  double pore_connect_avg( 0.0);
157  double d_eff_avg( 0.0);
158  double wfps_avg( 0.0);
159  double air_avg( 0.0);
160  double root_conduct_avg( 0.0);
161  double o2_sum( 0.0);
162  double depth_sum( 0.0);
163 
164  double nitrification_inhibition( 0.0);
165  double urease_inhibition( 0.0);
166 
167  double mineral_efficiency_scale_sum( 0.0);
168  double mineral_efficiency( 0.0);
169  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
170  {
171  double const c_mic_sum( sc_.C_micro1_sl[sl] + sc_.C_micro2_sl[sl] + sc_.C_micro3_sl[sl]);
172  double const n_mic_sum( n_micro_1_sl[sl] + n_micro_2_sl[sl] + n_micro_3_sl[sl]);
173  mineral_efficiency += MeTrX_get_mineral_efficiency( c_mic_sum / n_mic_sum, cn_opt_mic_sl[sl]) * c_mic_sum;
174  mineral_efficiency_scale_sum += c_mic_sum;
175 
176  anvf_avg += sc_.anvf_sl[sl] * sc_.h_sl[sl];
177 #ifdef METRX_ANVF_TYPES
178  anvf_avg_pnet += anvf_pnet_sl[sl] * sc_.h_sl[sl];
179  anvf_avg_dndc_can += anvf_dndccan_sl[sl] * sc_.h_sl[sl];
180  anvf_avg_nloss += anvf_nloss_sl[sl] * sc_.h_sl[sl];
181 #endif
182  pore_connect_avg += pore_connectivity_sl[sl] * sc_.h_sl[sl];
183  d_eff_avg += D_eff_air_sl[sl] * sc_.h_sl[sl];
184  wfps_avg += MeTrX_get_wfps( sl) * sc_.h_sl[sl];
185  air_avg += (v_air_sl[sl] / sc_.h_sl[sl]) * sc_.h_sl[sl];
186  root_conduct_avg += D_eff_plant_sl[sl] * sc_.h_sl[sl];
187  o2_sum += o2_gas_sl[sl] + o2_liq_sl[sl];
188  depth_sum += sc_.h_sl[sl];
189 
190  if ( cbm::flt_less_equal( sc_.depth_sl[sl], 0.2))
191  {
192  soc20 += (sc_.C_aorg_sl[sl] +c_humus_1_sl[sl]+c_humus_2_sl[sl]+c_humus_3_sl[sl]
193  +sc_.C_micro1_sl[sl]+sc_.C_micro2_sl[sl]+sc_.C_micro3_sl[sl]
194  +sc_.C_lit1_sl[sl]+sc_.C_lit2_sl[sl]+sc_.C_lit3_sl[sl]);
195  totn20 += (sc_.N_aorg_sl[sl] +n_humus_1_sl[sl]+n_humus_2_sl[sl]+n_humus_3_sl[sl]
196  +sc_.N_micro_sl[sl] +sc_.N_lit1_sl[sl]+sc_.N_lit2_sl[sl]+sc_.N_lit3_sl[sl]);
197  soilmass20 += (sc_.dens_sl[sl] * cbm::DM3_IN_M3 * sc_.h_sl[sl]);
198  }
199 
200  if ( cbm::flt_less_equal( sc_.depth_sl[sl], 0.4))
201  {
202  soc40 += (sc_.C_aorg_sl[sl] +c_humus_1_sl[sl]+c_humus_2_sl[sl]+c_humus_3_sl[sl]
203  +sc_.C_micro1_sl[sl]+sc_.C_micro2_sl[sl]+sc_.C_micro3_sl[sl]
204  +sc_.C_lit1_sl[sl]+sc_.C_lit2_sl[sl]+sc_.C_lit3_sl[sl]);
205  totn40 += (sc_.N_aorg_sl[sl] +n_humus_1_sl[sl]+n_humus_2_sl[sl]+n_humus_3_sl[sl]
206  +sc_.N_micro_sl[sl] +sc_.N_lit1_sl[sl]+sc_.N_lit2_sl[sl]+sc_.N_lit3_sl[sl]);
207  soilmass40 += (sc_.dens_sl[sl] * cbm::DM3_IN_M3 * sc_.h_sl[sl]);
208  }
209  }
210 
211  int sl_counter( 0);
212  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
213  {
214  double const ni_inhibition( crnf_.get_nitrification_inhibition( sc_.ni_sl[sl]));
215  if ( cbm::flt_greater_zero( ni_inhibition))
216  {
217  sl_counter += 1;
218  nitrification_inhibition += ni_inhibition;
219  }
220  }
221 
222  if ( sl_counter > 0)
223  {
224  nitrification_inhibition /= sl_counter;
225  urease_inhibition /= sl_counter;
226  }
227 
228  double const litter_height( (sl_.soil_layers_in_litter_cnt() > 0) ? sc_.depth_sl[sl_.soil_layers_in_litter_cnt()-1] : 0.0);
229  anvf_avg /= depth_sum;
230 #ifdef METRX_ANVF_TYPES
231  anvf_avg_pnet /= depth_sum;
232  anvf_avg_dndc_can /= depth_sum;
233  anvf_avg_nloss /= depth_sum;
234 #endif
235  pore_connect_avg /= depth_sum;
236  d_eff_avg /= depth_sum;
237  wfps_avg /= depth_sum;
238  air_avg /= depth_sum;
239  root_conduct_avg /= depth_sum;
240 
241  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( anvf_avg);
242 #ifdef METRX_ANVF_TYPES
243  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( anvf_avg_pnet);
244  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( anvf_avg_dndc_can);
245  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( anvf_avg_nloss);
246 #endif
247  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( pore_connect_avg);
248  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( d_eff_avg);
249  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( wfps_avg);
250  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( air_avg);
251  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( root_conduct_avg);
252  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( o2_sum * cbm::M2_IN_HA);
253  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( crnf_.get_crnf_teff_mean());
254  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( crnf_.get_crnf_release_fraction_mean());
255  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nitrification_inhibition);
256  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( urease_inhibition);
257  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( mineral_efficiency / (mineral_efficiency_scale_sum * sl_.soil_layer_cnt()));
258  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( don_sum * cbm::M2_IN_HA);
259  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh4_sum * cbm::M2_IN_HA);
260  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh4_clay_sum * cbm::M2_IN_HA);
261  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( coated_nh4_sum * cbm::M2_IN_HA);
262  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( urea_sum * cbm::M2_IN_HA);
263  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no2_sum * cbm::M2_IN_HA);
264  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( an_no2_sum * cbm::M2_IN_HA);
265  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no3_sum * cbm::M2_IN_HA);
266  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( an_no3_sum * cbm::M2_IN_HA);
267  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n2o_sum * cbm::M2_IN_HA);
268  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( an_n2o_sum * cbm::M2_IN_HA);
269  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no_sum * cbm::M2_IN_HA);
270  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( an_no_sum * cbm::M2_IN_HA);
271  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh3_gas_sum * cbm::M2_IN_HA);
272  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh3_liq_sum * cbm::M2_IN_HA);
273  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( doc_sum * cbm::M2_IN_HA);
274  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( an_doc_sum * cbm::M2_IN_HA);
275  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( acetate_sum * cbm::M2_IN_HA);
276  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ch4_gas_sum * cbm::M2_IN_HA);
277  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ch4_liq_sum * cbm::M2_IN_HA);
278  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( caorg * cbm::M2_IN_HA);
279  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( naorg * cbm::M2_IN_HA);
280  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( cmic1 * cbm::M2_IN_HA);
281  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( cmic2 * cbm::M2_IN_HA);
282  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( cmic3 * cbm::M2_IN_HA);
283  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nmic1 * cbm::M2_IN_HA);
284  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nmic2 * cbm::M2_IN_HA);
285  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nmic3 * cbm::M2_IN_HA);
286  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( chum1 * cbm::M2_IN_HA);
287  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( chum2 * cbm::M2_IN_HA);
288  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( chum3 * cbm::M2_IN_HA);
289  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nhum1 * cbm::M2_IN_HA);
290  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nhum2 * cbm::M2_IN_HA);
291  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nhum3 * cbm::M2_IN_HA);
292  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( clit1 * cbm::M2_IN_HA);
293  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( clit2 * cbm::M2_IN_HA);
294  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( clit3 * cbm::M2_IN_HA);
295  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nlit1 * cbm::M2_IN_HA);
296  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nlit2 * cbm::M2_IN_HA);
297  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nlit3 * cbm::M2_IN_HA);
298  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_algae_tot * cbm::M2_IN_HA);
299  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n_algae_tot * cbm::M2_IN_HA);
300  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( cstub * cbm::M2_IN_HA);
301  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nstub * cbm::M2_IN_HA);
302  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (cwood+caorg+cmic1+cmic2+cmic3+chum1+chum2+chum3+clit1+clit2+clit3+c_algae+cstub+csol) * cbm::M2_IN_HA);
303  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (nwood+naorg+nmic1+nmic2+nmic3+nhum1+nhum2+nhum3+nlit1+nlit2+nlit3+n_algae+nstub+nsol) * cbm::M2_IN_HA);
304 
305  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n_sbl * cbm::M2_IN_HA);
306 
307  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( soc20 / soilmass20);
308  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( soc40 / soilmass40);
309  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( totn20 / soilmass20);
310  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( totn40 / soilmass40);
311  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.fe2_sl.sum() * cbm::M2_IN_HA);
312  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.fe3_sl.sum() * cbm::M2_IN_HA);
313  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.till_effect_sl.sum() / sl_.soil_layer_cnt());
314  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( freeze_thaw_fact_sl.sum());
315  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( litter_height);
316  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( MeTrX_get_ph_wl());
317  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.ph_sl[0]);
318  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_no3_groundwater_access * cbm::M2_IN_HA);
319  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (day_assi_n_mic_1+day_assi_n_mic_2+day_assi_n_mic_3) * cbm::M2_IN_HA);
320  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_nit_nh4_no2 * cbm::M2_IN_HA);
321  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_nit_no2_no3_sl.sum() * cbm::M2_IN_HA);
322  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_nit_no2_no * cbm::M2_IN_HA);
323  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_nit_no2_n2o * cbm::M2_IN_HA);
324  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_no3_no2 * cbm::M2_IN_HA);
325  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_no2_no * cbm::M2_IN_HA);
326  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_no2_n2o * cbm::M2_IN_HA);
327  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_no2_n2 * cbm::M2_IN_HA);
328  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_no_n2o * cbm::M2_IN_HA);
329  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_no_n2 * cbm::M2_IN_HA);
330  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_n2o_n2 * cbm::M2_IN_HA);
331  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_chemodenit_no2_no * cbm::M2_IN_HA);
332  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_ch4_oxidation_sl.sum() * cbm::M2_IN_HA);
333  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_ch4_production_hydrogen_sl.sum() * cbm::M2_IN_HA);
334  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_ch4_production_acetate_sl.sum() * cbm::M2_IN_HA);
335  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_plant.sum() * cbm::M2_IN_HA);
336  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_soil.sum() * cbm::M2_IN_HA);
337  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_water.sum() * cbm::M2_IN_HA);
338  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_bubbling.sum() * cbm::M2_IN_HA);
339  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_leach.sum() * cbm::M2_IN_HA);
340  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_o2_plant.sum() * cbm::M2_IN_HA);
341 
342  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (sc_.accumulated_c_litter_stubble + sc_.accumulated_c_litter_wood_above - accumulated_c_litter_above_old) * cbm::M2_IN_HA);
343  accumulated_c_litter_above_old = sc_.accumulated_c_litter_stubble + sc_.accumulated_c_litter_wood_above;
344 
345  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (sc_.accumulated_c_litter_below_sl.sum() + sc_.accumulated_c_litter_wood_below_sl.sum() - accumulated_c_litter_below_old) * cbm::M2_IN_HA);
346  accumulated_c_litter_below_old = sc_.accumulated_c_litter_below_sl.sum() + sc_.accumulated_c_litter_wood_below_sl.sum();
347 
348  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_fix_algae * cbm::M2_IN_HA);
349  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_n_fix_algae * cbm::M2_IN_HA);
350  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (day_decomp_c_lit_1+day_decomp_c_lit_2+day_decomp_c_lit_3) * cbm::M2_IN_HA);
351  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_decay_c_mic_sl.sum()*cbm::M2_IN_HA);
352  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_mic_1_growth * cbm::M2_IN_HA);
353  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_mic_1_maintenance * cbm::M2_IN_HA);
354  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_mic_2 * cbm::M2_IN_HA);
355  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_mic_3_acetate_prod * cbm::M2_IN_HA);
356  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_mic_3_acetate_cons * cbm::M2_IN_HA);
357  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_ch4_prod * cbm::M2_IN_HA);
358  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_co2_prod_ch4_cons * cbm::M2_IN_HA);
359  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_h2_c_eq_prod_sl.sum() * cbm::M2_IN_HA);
360  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_acetate_prod_sl.sum() * cbm::M2_IN_HA);
361  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_acetate_cons_fe3_sl.sum() * cbm::M2_IN_HA/FE3_ACETATE_REDUCTION_RATIO);
362  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_h2_c_eq_cons_fe3_sl.sum() * cbm::M2_IN_HA/FE3_ACETATE_REDUCTION_RATIO);
363  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_doc_prod_decomp_litter * cbm::M2_IN_HA);
364  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_doc_prod_decomp_humus * cbm::M2_IN_HA);
365  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_doc_prod_decomp_aorg * cbm::M2_IN_HA);
366  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( dC_root_exsudates * cbm::M2_IN_HA);
367  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_doc_prod_sl.sum() * cbm::M2_IN_HA);
368  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_doc_hum_1_sl.sum() * cbm::M2_IN_HA);
369  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_sol_hum_1_sl.sum() * cbm::M2_IN_HA);
370  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_cel_hum_1_sl.sum() * cbm::M2_IN_HA);
371  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_lig_hum_1_sl.sum() * cbm::M2_IN_HA);
372  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_lig_hum_2_sl.sum() * cbm::M2_IN_HA);
373  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_mic_hum_1_sl.sum() * cbm::M2_IN_HA);
374  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_mic_hum_2_sl.sum() * cbm::M2_IN_HA);
375  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_hum_1_hum_2_sl.sum() * cbm::M2_IN_HA);
376  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_c_humify_hum_2_hum_3_sl.sum() * cbm::M2_IN_HA);
377  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_min_n_decomp * cbm::M2_IN_HA);
378  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_min_n_aorg * cbm::M2_IN_HA);
379  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_min_n_mic_1 * cbm::M2_IN_HA);
380  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_min_n_mic_2 * cbm::M2_IN_HA);
381  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_min_n_mic_3 * cbm::M2_IN_HA);
382  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_assi_c_mic_1 * cbm::M2_IN_HA);
383  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_assi_c_mic_2 * cbm::M2_IN_HA);
384  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_assi_c_mic_3 * cbm::M2_IN_HA);
385 
386  return output_writer_.write_daily( output_data_);
387 }
ldndc::SoilChemistryMeTrX::MeTrX_get_ph_wl
double MeTrX_get_ph_wl()
Definition: soilchemistry-metrx-physics-chemistry.cpp:524
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◆ MeTrX_write_output_fluxes()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_fluxes ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_write_output().

699 {
700 #define METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH(__val__) \
701 { \
702 double const delta_val( __val__ - output_writer_.output_writer_fluxes.__val__); \
703 LDNDC_OUTPUT_SET_COLUMN_((delta_val),=,output_data_,1); \
704 output_writer_.output_writer_fluxes.__val__ = __val__; \
705 } \
706 
707 #define METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH_2(__val1__,__val2__) \
708 { \
709 double const delta_val( __val1__ - output_writer_.output_writer_fluxes.__val2__); \
710 LDNDC_OUTPUT_SET_COLUMN_((delta_val),=,output_data_,1); \
711 output_writer_.output_writer_fluxes.__val2__ = __val1__; \
712 } \
713 
714  for ( size_t l = 0; l < sl_.soil_layer_cnt(); ++l)
715  {
716  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
717  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( -sc_.depth_sl[l]);
718 
719  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_throughfall_sl[l]);
720  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_throughfall_sl[l]);
721  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_throughfall_sbl[l]);
722  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_throughfall_sbl[l]);
723 
724  //N fluxes in plant/algae
725  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_to_living_plant_and_algae_from_extern_sl[l]);
726  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH_2( ph_.accumulated_nh4_uptake_sl[l], accumulated_n_plant_nh4_uptake_sl[l]);
727  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH_2( ph_.accumulated_no3_uptake_sl[l], accumulated_n_plant_no3_uptake_sl[l]);
728  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH_2( ph_.accumulated_nh3_uptake_sl[l], accumulated_n_plant_nh3_uptake_sl[l]);
729  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH_2( ph_.accumulated_don_uptake_sl[l], accumulated_n_plant_don_uptake_sl[l]);
730  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_algae_nh4_uptake_sbl[l]);
731  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_algae_no3_uptake_sbl[l]);
732  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_algae_nh3_uptake_sbl[l]);
733 
734  //N fluxes from plant to raw litter, stubble and wood
735  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_plants_below_rawlitter_sl[l]);
736  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_plants_below_wood_sl[l]);
737  if ( l == 0)
738  {
739  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_plants_above_rawlitter);
740  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_plants_above_wood);
741  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_plants_above_stubble);
742  }
743  else
744  {
745  LDNDC_OUTPUT_SET_COLUMN_(0.0,=,output_data_,1);
746  LDNDC_OUTPUT_SET_COLUMN_(0.0,=,output_data_,1);
747  LDNDC_OUTPUT_SET_COLUMN_(0.0,=,output_data_,1);
748  }
749 
750  //N fluxes from raw litter to soil litter
751  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aboveground_raw_litter_fragmentation_sl[l]);
752  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_belowground_raw_litter_fragmentation_sl[l]);
753 
754  //N fluxes from grazer and algae
755  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_algae_sl[l]);
756  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_from_dung_sl[l]);
757  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_from_dung_sl[l]);
758 
759  //N exported via harvesting, cutting and grazing
760  if ( l == 0)
761  {
762  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_export_harvest_cutting_grazing);
763  }
764  else
765  {
766  LDNDC_OUTPUT_SET_COLUMN_(0.0,=,output_data_,1);
767  }
768 
769  //N fluxes from fertilization and manuring
770  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_fertilization_sl[l]);
771  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_fertilization_sl[l]);
772  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_fertilization_sl[l]);
773  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_fertilization_sl[l]);
774  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_fertilization_sl[l]);
775  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_fertilization_sl[l]);
776  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_fertilization_sl[l]);
777  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_fertilization_sbl[l]);
778  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_fertilization_sbl[l]);
779  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_fertilization_sbl[l]);
780  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_fertilization_sbl[l]);
781 
782  //N redistribution during tilling
783  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_surface_litter_incorporation_via_tilling_sl[l]);
784  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_tilling_sl[l]);
785  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_tilling_sl[l]);
786  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_1_tilling_sl[l]);
787  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_2_tilling_sl[l]);
788  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_3_tilling_sl[l]);
789  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_tilling_sl[l]);
790  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no2_tilling_sl[l]);
791  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_tilling_sl[l]);
792  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_tilling_sl[l]);
793  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_tilling_sl[l]);
794  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_tilling_sl[l]);
795  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_tilling_sl[l]);
796  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_tilling_sl[l]);
797  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_microbes_tilling_sl[l]);
798 
799  //N redistribution during spin up
800  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_1_spinup_sl[l]);
801  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_2_spinup_sl[l]);
802  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_3_spinup_sl[l]);
803  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_surface_litter_spinup_sl[l]);
804  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_spinup_sl[l]);
805 
806  //N fluxes due to water movement
807  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_micro_leaching_sl[l]);
808  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_leaching_sl[l]);
809  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_leaching_sl[l]);
810  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_1_leaching_sl[l]);
811  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_2_leaching_sl[l]);
812  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_3_leaching_sl[l]);
813  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_leaching_sl[l]);
814  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH_2( sc_.accumulated_n_no3_leaching_sl[l], accumulated_n_no3_leaching_sl[l]);
815  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_leaching_sl[l]);
816  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_leaching_sl[l]);
817  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_leaching_sl[l]);
818  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_leaching_sl[l]);
819  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_leaching_sl[l]);
820 
821  //N fluxes via liquid diffusion
822  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_liq_diffusion_sl[l]);
823  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_liq_diffusion_sl[l]);
824  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_liq_diffusion_sl[l]);
825  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_liq_diffusion_sl[l]);
826 
827  // incoming N from leaching from surface water
828  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_infiltration_phys_sl[l]);
829  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_infiltration_phys_sl[l]);
830  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_infiltration_phys_sl[l]);
831  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_infiltration_phys_sl[l]);
832  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_infiltration_phys_sl[l]);
833  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_infiltration_phys_sl[l]);
834 
835  //incoming N fluxes from disappearing water table
836  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_infiltration_leach_sl[l]);
837  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_infiltration_leach_sl[l]);
838  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_infiltration_leach_sl[l]);
839  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_infiltration_leach_sl[l]);
840  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_infiltration_leach_sl[l]);
841  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_infiltration_leach_sl[l]);
842  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_infiltration_leach_sl[l]);
843 
844  //incoming N flux via liquid diffusion from surface water
845  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_infiltration_liqdif_sl[l]);
846  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_infiltration_liqdif_sl[l]);
847  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_infiltration_liqdif_sl[l]);
848  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_infiltration_liqdif_sl[l]);
849 
850  //ebullition fluxes
851  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_bubbling_sl[l]);
852  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_bubbling_sl[l]);
853  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_bubbling_sl[l]);
854  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_bubbling_sbl[l]);
855  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_bubbling_sbl[l]);
856  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_bubbling_sbl[l]);
857 
858  //N fluxes due to dissolution between atmosphere and surface water
859  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_dissolution_sbl[l]);
860  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_dissolution_sbl[l]);
861  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_dissolution_sbl[l]);
862 
863  //N fluxes from urea to nh4
864  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_nh4_hydrolysis_sl[l]);
865  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_urea_nh4_hydrolysis_sbl[l]);
866 
867  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_assimilation_sl[l]);
868  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_assimilation_sl[l]);
869  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_assimilation_sl[l]);
870 
871  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_nh3_conversion_sl[l]);
872  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_nh4_conversion_sl[l]);
873  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_nh3_conversion_sbl[l]);
874  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_nh4_conversion_sbl[l]);
875 
876  //gaseous diffusion
877  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_phys_diffusion_sl[l]);
878  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_phys_diffusion_sl[l]);
879  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_phys_diffusion_sl[l]);
880  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh3_gas_diffusion_sl[l]);
881  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_gas_diffusion_sl[l]);
882  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_gas_diffusion_sl[l]);
883 
884  //perturbation
885  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_micro_perturbation_sl[l]);
886  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_perturbation_sl[l]);
887  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_perturbation_sl[l]);
888  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_1_perturbation_sl[l]);
889  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_2_perturbation_sl[l]);
890  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_3_perturbation_sl[l]);
891 
892  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_no2_nitrification_sl[l]);
893  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_no_nitrification_sl[l]);
894  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_nh4_n2o_nitrification_sl[l]);
895  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no2_no3_nitrification_sl[l]);
896 
897  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_no2_denitrification_sl[l]);
898  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_no_denitrification_sl[l]);
899  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_n2o_denitrification_sl[l]);
900  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no3_n2_denitrification_sl[l]);
901  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no2_no_denitrification_sl[l]);
902  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no2_n2o_denitrification_sl[l]);
903  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no2_n2_denitrification_sl[l]);
904  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_n2o_denitrification_sl[l]);
905  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no_n2_denitrification_sl[l]);
906  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_n2o_n2_denitrification_sl[l]);
907 
908  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_no2_chemodenitrification_sl[l]);
909 
910  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_mic_naorg_decay_sl[l]);
911  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_mic_nh4_mineral_sl[l]);
912  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_mic_don_dissolve_sl[l]);
913 
914  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_nh4_mineral_sl[l]);
915  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_aorg_don_dissolve_sl[l]);
916 
917  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_1_don_dissolve_sl[l]);
918  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_1_nh4_mineral_sl[l]);
919  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_2_don_dissolve_sl[l]);
920  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_2_nh4_mineral_sl[l]);
921  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_3_don_dissolve_sl[l]);
922  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_humus_3_nh4_mineral_sl[l]);
923 
924  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_don_dissolve_sl[l]);
925  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_nh4_mineral_sl[l]);
926 
927  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_humus_1_humify_sl[l]);
928  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_humus_2_humify_sl[l]);
929  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_don_humus_3_humify_sl[l]);
930  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT_AND_SWITCH( accumulated_n_litter_humus_1_humify_sl[l]);
931 
932  lerr_t rc_write = output_writer_.write_fluxes( l, output_data_);
933  if ( rc_write)
934  {
935  return LDNDC_ERR_FAIL;
936  }
937  }
938 
939  return LDNDC_ERR_OK;
940 }
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◆ MeTrX_write_output_layer_daily()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_layer_daily ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_get_ph_wl().

Referenced by MeTrX_write_output().

436 {
437  size_t fl_cnt( m_veg->canopy_layers_used());
438  size_t sbl_cnt( sb_.surfacebulk_layer_cnt());
439 
440  for ( size_t fl = fl_cnt; fl > 0; --fl)
441  {
442  size_t l( fl-1);
443  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
444  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //depth
445  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ph_.h_fl[fl]); //extension
446  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //pH
447  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //pore_connectivity
448  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( D_eff_air_fl[l]); //air permeability
449  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //aerenchym_permeability
450  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //cfdd
451  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //water_content
452  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //air_content
453  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //porosity
454  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //fe2
455  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //fe3
456  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ts_co2_concentration_fl[l]*cbm::M2_IN_HA);
457  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ts_ch4_concentration_fl[l]*cbm::M2_IN_HA);
458  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //ch4 bubbling
459  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //ch4 production
460  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //ch4 oxidation
461  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //doc production
462  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //acetate production
463  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //mic decay
464  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //doc
465  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //acetate
466  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3
467  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //nh4
468  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //urea
469  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh3_fl[l]*cbm::M2_IN_HA);
470  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //o2
471  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ts_no_concentration_fl[l]*cbm::M2_IN_HA);
472  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //n2o
473  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //c_humus_0
474  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //c_humus_1
475  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //c_humus_2
476  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3_cons_denit
477  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //denit_factor_c
478  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //denit_factor_n
479  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3_prod_nit
480  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3_leaching
481 
482  lerr_t rc_write = output_writer_.write_layer_daily( -static_cast< int >( fl+sbl_cnt+1), output_data_);
483  if ( rc_write)
484  {
485  return LDNDC_ERR_FAIL;
486  }
487  }
488 
489  for (size_t sbl = sbl_cnt; sbl > 0; --sbl)
490  {
491  double depth_sbl( sbl_cnt * 0.01 - 0.5 * 0.01 - (sbl-1) * 0.01);
492  size_t l( sbl-1);
493  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
494  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( depth_sbl); //depth
495  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //extension
496  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( MeTrX_get_ph_wl()); //pH
497  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //pore_connectivity
498  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //air permeability
499  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //aerenchym_permeability
500  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //cfdd
501  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //water_content
502  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //air_content
503  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //porosity
504  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //fe2
505  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //fe3
506  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.co2_sbl[l]*cbm::M2_IN_HA);
507  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.ch4_sbl[l]*cbm::M2_IN_HA);
508 
509  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (accumulated_c_ch4_bubbling_sbl[l]-
510  output_writer_.output_writer_layer_daily.accumulated_c_ch4_bubbling_sbl[l])*cbm::M2_IN_HA);
511  output_writer_.output_writer_layer_daily.accumulated_c_ch4_bubbling_sbl[l] = accumulated_c_ch4_bubbling_sbl[l];
512 
513  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //ch4 production
514  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //ch4 oxidation
515  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //doc production
516  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //acetate production
517  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //mic decay
518  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.doc_sbl[l]*cbm::M2_IN_HA);
519  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //acetate
520  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.no3_sbl[l]*cbm::M2_IN_HA);
521  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.nh4_sbl[l]*cbm::M2_IN_HA);
522  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.urea_sbl[l]*cbm::M2_IN_HA);
523  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.nh3_sbl[l]*cbm::M2_IN_HA);
524  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.o2_sbl[l]*cbm::M2_IN_HA);
525  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no
526  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //n2o
527  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //c_humus_0
528  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //c_humus_1
529  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //c_humus_2
530  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3_cons_denit
531  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //denit_factor_c
532  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //denit_factor_n
533  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3_prod_nit
534  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0.0); //no3_leaching
535 
536  lerr_t rc_write = output_writer_.write_layer_daily( -static_cast< int >( sbl), output_data_);
537  if ( rc_write)
538  {
539  return LDNDC_ERR_FAIL;
540  }
541  }
542 
543  for ( size_t l = 0; l < sl_.soil_layer_cnt(); ++l)
544  {
545  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
546  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( -sc_.depth_sl[l]);
547  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.h_sl[l]);
548  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.ph_sl[l]);
549  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( pore_connectivity_sl[l]);
550  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( D_eff_air_sl[l]);
551  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( D_eff_plant_sl[l]);
552  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( cumulative_freezing_degree_days_sl[l]);
553  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( wc_.wc_sl[l]);
554  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( v_air_sl[l]/sc_.h_sl[l]);
555  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.poro_sl[l]);
556  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.fe2_sl[l]*cbm::M2_IN_HA);
557  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.fe3_sl[l]*cbm::M2_IN_HA);
558  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (co2_liq_sl[l]+co2_gas_sl[l])*cbm::M2_IN_HA);
559  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (ch4_liq_sl[l]+ch4_gas_sl[l])*cbm::M2_IN_HA);
560  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (accumulated_c_ch4_bubbling_sl[l]-
561  output_writer_.output_writer_layer_daily.accumulated_c_ch4_bubbling_sl[l])*cbm::M2_IN_HA);
562  output_writer_.output_writer_layer_daily.accumulated_c_ch4_bubbling_sl[l] = accumulated_c_ch4_bubbling_sl[l];
563  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (day_ch4_production_acetate_sl[l]+day_ch4_production_hydrogen_sl[l])*cbm::M2_IN_HA);
564  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_ch4_oxidation_sl[l]*cbm::M2_IN_HA);
565  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_doc_prod_sl[l]*cbm::M2_IN_HA);
566  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_acetate_prod_sl[l]*cbm::M2_IN_HA);
567  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_decay_c_mic_sl[l]*cbm::M2_IN_HA);
568  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (sc_.doc_sl[l]+sc_.an_doc_sl[l])*cbm::M2_IN_HA);
569  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (ae_acetate_sl[l]+an_acetate_sl[l])*cbm::M2_IN_HA);
570  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (no3_ae_sl[l]+no3_an_sl[l])*cbm::M2_IN_HA);
571  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (nh4_ae_sl[l]+nh4_an_sl[l]+sc_.clay_nh4_sl[l])*cbm::M2_IN_HA);
572  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.urea_sl[l]*cbm::M2_IN_HA);
573  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (sc_.nh3_gas_sl[l]+sc_.nh3_liq_sl[l])*cbm::M2_IN_HA);
574  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (o2_gas_sl[l]+o2_liq_sl[l])*cbm::M2_IN_HA);
575  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (no_liq_sl[l]+no_gas_sl[l]+an_no_liq_sl[l]+an_no_gas_sl[l])*cbm::M2_IN_HA);
576  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (n2o_liq_sl[l]+n2o_gas_sl[l]+an_n2o_liq_sl[l]+an_n2o_gas_sl[l])*cbm::M2_IN_HA);
577  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_humus_1_sl[l]*cbm::M2_IN_HA);
578  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_humus_2_sl[l]*cbm::M2_IN_HA);
579  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_humus_3_sl[l]*cbm::M2_IN_HA);
580  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (accumulated_n_no3_no2_denitrification_sl[l]
581  -output_writer_.output_writer_layer_daily.accumulated_n_no3_no2_denitrification_sl[l]) * cbm::M2_IN_HA);
582  output_writer_.output_writer_layer_daily.accumulated_n_no3_no2_denitrification_sl[l] = accumulated_n_no3_no2_denitrification_sl[l];
583  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_factor_c_sl[l]*FTS_TOT_);
584  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_denit_factor_n_sl[l]*FTS_TOT_);
585  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( day_nit_no2_no3_sl[l]*cbm::M2_IN_HA);
586  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( (sc_.accumulated_n_no3_leaching_sl[l]
587  -output_writer_.output_writer_layer_daily.accumulated_n_no3_leaching_sl[l]) * cbm::M2_IN_HA);
588  output_writer_.output_writer_layer_daily.accumulated_n_no3_leaching_sl[l] = sc_.accumulated_n_no3_leaching_sl[l];
589 
590  lerr_t rc_write = output_writer_.write_layer_daily( l, output_data_);
591  if ( rc_write)
592  {
593  return LDNDC_ERR_FAIL;
594  }
595  }
596 
597  return LDNDC_ERR_OK;
598 }
ldndc::SoilChemistryMeTrX::MeTrX_get_ph_wl
double MeTrX_get_ph_wl()
Definition: soilchemistry-metrx-physics-chemistry.cpp:524
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◆ MeTrX_write_output_layer_yearly()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_layer_yearly ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_write_output().

603 {
604  for ( size_t l = 0; l < sl_.soil_layer_cnt(); ++l)
605  {
606  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
607  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( -sc_.depth_sl[l]);
608  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_humus_1_sl[l]);
609  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_humus_2_sl[l]);
610  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_humus_3_sl[l]);
611  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.C_aorg_sl[l]);
612  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.C_micro1_sl[l]+sc_.C_micro2_sl[l]+sc_.C_micro3_sl[l]);
613 
614  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( accumulated_n_no3_no2_denitrification_sl[l] - output_writer_.output_writer_layer_yearly.accumulated_n_no3_no2_denitrification_sl[l]);
615  output_writer_.output_writer_layer_yearly.accumulated_n_no3_no2_denitrification_sl[l] = accumulated_n_no3_no2_denitrification_sl[l];
616 
617  lerr_t rc_write = output_writer_.write_layer_yearly( l, output_data_);
618  if ( rc_write)
619  {
620  return LDNDC_ERR_FAIL;
621  }
622  }
623 
624  return LDNDC_ERR_OK;
625 }
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◆ MeTrX_write_output_pools()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_pools ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_write_output().

630 {
631  for ( size_t l = 0; l < sl_.soil_layer_cnt(); ++l)
632  {
633  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
634  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( -sc_.depth_sl[l]);
635 
636  //pools that exist for each soil layer
637  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.urea_sl[l]);
638  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.N_lit1_sl[l] + sc_.N_lit2_sl[l] + sc_.N_lit3_sl[l] + sc_.n_wood_sl[l] + sc_.n_raw_lit_1_sl[l] + sc_.n_raw_lit_2_sl[l] + sc_.n_raw_lit_3_sl[l]);
639  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.N_aorg_sl[l]);
640  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n_humus_1_sl[l]);
641  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n_humus_2_sl[l]);
642  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n_humus_3_sl[l]);
643  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n_micro_1_sl[l] + n_micro_2_sl[l] + n_micro_3_sl[l]);
644  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.nh3_liq_sl[l] + sc_.nh3_gas_sl[l]);
645  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh4_ae_sl[l] + nh4_an_sl[l] + sc_.clay_nh4_sl[l]);
646  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( don_ae_sl[l] + don_an_sl[l]);
647  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no3_ae_sl[l] + no3_an_sl[l]);
648  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.no2_sl[l] + sc_.an_no2_sl[l]);
649  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no_gas_sl[l] + an_no_gas_sl[l] + no_liq_sl[l] + an_no_liq_sl[l]);
650  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( n2o_gas_sl[l] + an_n2o_gas_sl[l] + n2o_liq_sl[l] + an_n2o_liq_sl[l]);
651 
652  //surface pools
653  if( l == 0 )
654  {
655  double nplant(0.0);
656  for ( PlantIterator vt = this->m_veg->begin(); vt != this->m_veg->end(); ++vt)
657  {
658  nplant += (*vt)->total_nitrogen();
659  }
660 
661  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.nh4_sbl.sum() );
662  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.nh3_sbl.sum() );
663  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.n2o_sbl.sum() );
664  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.no_sbl.sum() );
665  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.urea_sbl.sum() );
666  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.no3_sbl.sum() );
667  //METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sb_.don_sbl.sum() );
668  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nplant );
669  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.n_wood + sc_.n_stubble_lit1 + sc_.n_stubble_lit2 + sc_.n_stubble_lit3 +
670  sc_.n_raw_lit_1_above + sc_.n_raw_lit_2_above + sc_.n_raw_lit_3_above);
671  }
672  else
673  {
674  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
675  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
676  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
677  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
678  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
679  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
680  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
681  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
682  //METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
683  //METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( 0 );
684  }
685 
686  lerr_t rc_write = output_writer_.write_pools( l, output_data_);
687  if ( rc_write)
688  {
689  return LDNDC_ERR_FAIL;
690  }
691  }
692 
693  return LDNDC_ERR_OK;
694 }
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◆ MeTrX_write_output_subdaily()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_subdaily ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_get_ph_wl().

Referenced by MeTrX_write_output().

945 {
946  size_t s( lclock()->subday()-1);
947  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
948  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.C_micro1_sl.sum());
949  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.C_micro2_sl.sum());
950  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.C_micro3_sl.sum());
951  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.C_aorg_sl.sum());
952  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( nh4_ae_sl.sum()+nh4_an_sl.sum()+sc_.clay_nh4_sl.sum());
953  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no3_ae_sl.sum());
954  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( no3_an_sl.sum());
955  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.doc_sl.sum());
956  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.an_doc_sl.sum());
957  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( ae_acetate_sl.sum());
958  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( an_acetate_sl.sum());
959 
960  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_bubbling[s]);
961  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_plant[s]);
962  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_soil[s]);
963  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_water[s]);
964  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_leach[s]);
965  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_prod[s]);
966  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_ch4_ox[s]);
967 
968  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_acetate_prod[s]);
969  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_doc_prod[s]);
970 
971  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( accumulated_n_no2_no3_nitrification_sl.sum() - output_writer_.output_writer_subdaily.accumulated_n_no2_no3_nitrification);
972  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( accumulated_n_no3_no2_denitrification_sl.sum() - output_writer_.output_writer_subdaily.accumulated_n_no3_no2_denitrification);
973 
974  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_n2o_bubbling[s]);
975  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_n2o_plant[s]);
976  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_n2o_soil[s]);
977  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_n2o_water[s]);
978  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_no_bubbling[s]);
979  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_no_plant[s]);
980  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_no_soil[s]);
981  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_no_water[s]);
982  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_nh3_bubbling[s]);
983  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_nh3_plant[s]);
984  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_nh3_soil[s]);
985  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_nh3_water[s]);
986 
987  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_plant_o2_cons[s]);
988  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_o2_plant[s]);
989  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( subdaily_algae_o2_prod[s]);
990 
991  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( MeTrX_get_ph_wl());
992  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( sc_.ph_sl[0]);
993  double anvf_mean( sc_.anvf_sl.sum() / sl_.soil_layer_cnt());
994  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( anvf_mean);
995 
996  lerr_t rc_write = output_writer_.write_subdaily( output_data_);
997  if ( rc_write)
998  {
999  return LDNDC_ERR_FAIL;
1000  }
1001 
1002  output_writer_.output_writer_subdaily.accumulated_n_no2_no3_nitrification = accumulated_n_no2_no3_nitrification_sl.sum();
1003  output_writer_.output_writer_subdaily.accumulated_n_no3_no2_denitrification = accumulated_n_no3_no2_denitrification_sl.sum();
1004 
1005  return LDNDC_ERR_OK;
1006 }
ldndc::SoilChemistryMeTrX::MeTrX_get_ph_wl
double MeTrX_get_ph_wl()
Definition: soilchemistry-metrx-physics-chemistry.cpp:524
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◆ MeTrX_write_output_yearly()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_output_yearly ( )
private
Parameters
[in]None
[out]None
Returns
error code

Referenced by MeTrX_write_output().

392 {
393  double surface_litter( c_algae + c_dead_algae + sc_.c_stubble_lit1 + sc_.c_stubble_lit2 + sc_.c_stubble_lit3);
394  double soc20( 0.0);
395  double c_hum_1_20( 0.0);
396  double c_hum_2_20( 0.0);
397  double c_hum_3_20( 0.0);
398  double c_litter_20( 0.0);
399  double c_aorg_20( 0.0);
400  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
401  {
402  if ( cbm::flt_less_equal( sc_.depth_sl[sl], 0.2))
403  {
404  soc20 += sc_.C_aorg_sl[sl] + c_humus_1_sl[sl] + c_humus_2_sl[sl] + c_humus_3_sl[sl]
405  + sc_.C_micro1_sl[sl] + sc_.C_micro2_sl[sl] + sc_.C_micro3_sl[sl]
406  + sc_.C_lit1_sl[sl] + sc_.C_lit2_sl[sl] + sc_.C_lit3_sl[sl];
407  c_hum_1_20 += c_humus_1_sl[sl];
408  c_hum_2_20 += c_humus_2_sl[sl];
409  c_hum_3_20 += c_humus_3_sl[sl];
410  c_litter_20 += sc_.C_lit1_sl[sl] + sc_.C_lit2_sl[sl] + sc_.C_lit3_sl[sl];
411  c_aorg_20 += sc_.C_aorg_sl[sl];
412  }
413  else
414  {
415  break;
416  }
417  }
418 
419 #define METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT(__val__) LDNDC_OUTPUT_SET_COLUMN_((__val__),=,output_data_,1)
420  LDNDC_OUTPUT_SET_COLUMN_INDEX(0);
421 
422  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( surface_litter);
423  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( soc20);
424  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_hum_1_20);
425  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_hum_2_20);
426  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_hum_3_20);
427  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_litter_20);
428  METRX_OUTPUT_SET_COLUMN_AND_GOTO_NEXT( c_aorg_20);
429 
430  return output_writer_.write_yearly( output_data_);
431 }
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◆ MeTrX_write_rates()

lerr_t ldndc::SoilChemistryMeTrX::MeTrX_write_rates ( )
private
Parameters
[in]None
[out]None
Returns
error code

References MeTrX_send_state().

Referenced by solve().

20 {
21  sc_.accumulated_n2_emis = 0.0;
22  for( size_t sl = 0; sl < sl_.soil_layer_cnt(); ++sl)
23  {
24  sc_.no_sl[sl] = no_gas_sl[sl]+no_liq_sl[sl];
25  sc_.an_no_sl[sl] = an_no_gas_sl[sl]+an_no_liq_sl[sl];
26 
27  sc_.n2o_sl[sl] = n2o_gas_sl[sl]+n2o_liq_sl[sl];
28  sc_.an_n2o_sl[sl] = an_n2o_gas_sl[sl]+an_n2o_liq_sl[sl];
29 
30  sc_.C_hum_sl[sl] = c_humus_1_sl[sl] + c_humus_2_sl[sl] + c_humus_3_sl[sl];
31  sc_.N_hum_sl[sl] = n_humus_1_sl[sl] + n_humus_2_sl[sl] + n_humus_3_sl[sl];
32 
33  sc_.N_micro_sl[sl] = n_micro_1_sl[sl] + n_micro_2_sl[sl] + n_micro_3_sl[sl];
34  sc_.som_sl[sl] = (sc_.C_lit1_sl[sl] + sc_.C_lit2_sl[sl] + sc_.C_lit3_sl[sl]
35  + sc_.c_raw_lit_1_sl[sl] + sc_.c_raw_lit_2_sl[sl] + sc_.c_raw_lit_3_sl[sl]
36  + sc_.C_micro1_sl[sl] + sc_.C_micro2_sl[sl] + sc_.C_micro3_sl[sl]
37  + sc_.C_hum_sl[sl] + sc_.C_aorg_sl[sl])
38  / cbm::CCORG;
39 
40  sc_.o2_sl[sl] = o2_gas_sl[sl] * RGAS_M_O2_BAR_PA * (mc_temp_sl[sl] + cbm::D_IN_K) / v_air_sl[sl];
41 
42  sc_.accumulated_no3_denitrify_sl[sl] = accumulated_n_no3_no2_denitrification_sl[sl];
43  sc_.accumulated_n2_emis += accumulated_n_no3_n2_denitrification_sl[sl]
44  + accumulated_n_no2_n2_denitrification_sl[sl]
45  + accumulated_n_no_n2_denitrification_sl[sl]
46  + accumulated_n_n2o_n2_denitrification_sl[sl];
47  }
48 
49  size_t const ts_end( (timemode_ == TMODE_SUBDAILY) ? lclock()->subday() * INTERNAL_TIME_STEPS : INTERNAL_TIME_STEPS);
50  size_t const ts_start( ts_end - INTERNAL_TIME_STEPS);
51  for ( size_t ts = ts_start; ts < ts_end; ++ts)
52  {
53  sc_.accumulated_co2_emis += subdaily_co2_soil[ts] + subdaily_co2_plant[ts] + subdaily_co2_bubbling[ts] + subdaily_co2_water[ts];
54  sc_.accumulated_ch4_emis += subdaily_ch4_soil[ts] + subdaily_ch4_plant[ts] + subdaily_ch4_bubbling[ts] + subdaily_ch4_water[ts];
55  sc_.accumulated_n2o_emis += subdaily_n2o_soil[ts] + subdaily_n2o_plant[ts] + subdaily_n2o_bubbling[ts] + subdaily_n2o_water[ts];
56  sc_.accumulated_no_emis += subdaily_no_soil[ts] + subdaily_no_plant[ts] + subdaily_no_bubbling[ts] + subdaily_no_water[ts];
57  sc_.accumulated_nh3_emis += subdaily_nh3_soil[ts] + subdaily_nh3_plant[ts] + subdaily_nh3_bubbling[ts] + subdaily_nh3_water[ts];
58 
59  sc_.accumulated_ch4_leach += subdaily_ch4_leach[ts];
60  }
61 
62  sc_.accumulated_co2_emis_auto += co2_auto_sl.sum();
63  sc_.accumulated_co2_emis_hetero += co2_hetero_sl.sum();
64 
65  if (timemode_ == TMODE_SUBDAILY)
66  {
67  for ( PlantIterator vt = this->m_veg->begin(); vt != this->m_veg->end(); ++vt)
68  {
69  accumulated_n_to_living_plant_and_algae_from_extern_sl[0] += (*vt)->n2_fixation;
70  }
71  }
72  else
73  {
74  for ( PlantIterator vt = this->m_veg->begin(); vt != this->m_veg->end(); ++vt)
75  {
76  accumulated_n_to_living_plant_and_algae_from_extern_sl[0] += (*vt)->d_n2_fixation;
77  }
78  }
79 
80  if ( timemode_ != TMODE_SUBDAILY || lclock()->is_position( TMODE_POST_DAILY))
81  {
82  /*************************/
83  /* Yearly rate variables */
84  /*************************/
85 
86  sc_.accumulated_c_fix_algae += day_c_fix_algae;
87  sc_.accumulated_n_fix_algae += day_n_fix_algae;
88  }
89 
90  MeTrX_send_state();
91 
92  return LDNDC_ERR_OK;
93 }
ldndc::SoilChemistryMeTrX::MeTrX_send_state
lerr_t MeTrX_send_state()
Definition: soilchemistry-metrx-communicate.cpp:345
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◆ solve()

lerr_t ldndc::SoilChemistryMeTrX::solve ( )

Kicks off computation for one time step.

References MeTrX_algae_dynamics(), MeTrX_anaerobic_volume(), MeTrX_ch4_oxidation(), MeTrX_ch4_production(), MeTrX_check_for_negative_value(), MeTrX_chemodenitrification(), MeTrX_clay_nh4_equilibrium(), MeTrX_denitrification(), MeTrX_dissolution(), MeTrX_ebullition(), MeTrX_fermentation(), MeTrX_fertilize(), MeTrX_fragmentation(), MeTrX_freeze_thaw(), MeTrX_gas_diffusion(), MeTrX_groundwater_access(), MeTrX_iron_oxidation(), MeTrX_iron_reduction(), MeTrX_leaching(), MeTrX_liq_diffusion(), MeTrX_manure(), MeTrX_metabolism(), MeTrX_microbial_dynamics(), MeTrX_nh3_nh4_equilibrium(), MeTrX_nitrification(), MeTrX_nitrogen_fertilizer_release(), MeTrX_pertubation(), MeTrX_pH_calculation(), MeTrX_physics(), MeTrX_plant_respiration(), MeTrX_reset(), MeTrX_soil_organic_matter_turnover(), MeTrX_spinup(), MeTrX_till(), MeTrX_update(), MeTrX_urea_hydrolysis(), MeTrX_write_output(), and MeTrX_write_rates().

20 {
21  if ( (lclock()->subday() == 1) || (timemode_ != TMODE_SUBDAILY))
22  {
23  subdaily_time_step_ = 0;
24  }
25 
26  lerr_t rc = MeTrX_check_for_negative_value( "entry");
27  if ( rc) return LDNDC_ERR_FAIL;
28 
29  MeTrX_reset();
30 
31  rc = MeTrX_update();
32  if ( rc) return LDNDC_ERR_FAIL;
33 
34  rc = MeTrX_spinup();
35  if ( rc) return LDNDC_ERR_FAIL;
36 
37  rc = MeTrX_balance_check( 1);
38  if ( rc) return LDNDC_ERR_FAIL;
39 
40  rc = MeTrX_physics();
41  if ( rc) return LDNDC_ERR_FAIL;
42 
43  rc = MeTrX_fertilize();
44  if ( rc) return LDNDC_ERR_FAIL;
45 
46  rc = MeTrX_manure();
47  if ( rc) return LDNDC_ERR_FAIL;
48 
49  rc = MeTrX_till();
50  if ( rc) return LDNDC_ERR_FAIL;
51 
52  MeTrX_leaching();
53 
54  for (size_t ts = 0; ts < INTERNAL_TIME_STEPS; ++ts)
55  {
56  MeTrX_dissolution();
57  MeTrX_groundwater_access();
58  MeTrX_ebullition();
59  MeTrX_advection();
60  MeTrX_gas_diffusion();
61  MeTrX_liq_diffusion();
62 
63  MeTrX_anaerobic_volume();
64 
65  MeTrX_algae_dynamics();
66 
67  lerr_t rc_meta = MeTrX_metabolism();
68  if (rc_meta) { return rc_meta; }
69 
70  lerr_t rc_pertub = MeTrX_pertubation();
71  if (rc_pertub) { return rc_pertub; }
72 
73  MeTrX_nitrogen_fertilizer_release();
74  MeTrX_freeze_thaw();
75 
76  MeTrX_plant_respiration(ts);
77  MeTrX_fragmentation();
78  MeTrX_soil_organic_matter_turnover();
79  MeTrX_microbial_dynamics();
80 
81  MeTrX_nitrification();
82  MeTrX_denitrification();
83  MeTrX_chemodenitrification();
84  MeTrX_fermentation();
85 
86  MeTrX_urea_hydrolysis();
87  MeTrX_clay_nh4_equilibrium();
88  MeTrX_nh3_nh4_equilibrium();
89 
90  MeTrX_pH_calculation();
91 
92  MeTrX_iron_reduction();
93  MeTrX_iron_oxidation();
94 
95  MeTrX_ch4_production();
96  MeTrX_ch4_oxidation();
97 
98  subdaily_time_step_ += 1;
99  }
100 
101  rc = MeTrX_balance_check( 2);
102  if ( rc) return LDNDC_ERR_FAIL;
103 
104  MeTrX_write_rates();
105  MeTrX_write_output();
106 
107  rc = MeTrX_check_for_negative_value( "exit");
108  if ( rc) return LDNDC_ERR_FAIL;
109 
110  return LDNDC_ERR_OK;
111 }
ldndc::SoilChemistryMeTrX::MeTrX_update
lerr_t MeTrX_update()
Definition: soilchemistry-metrx-communicate.cpp:63
ldndc::SoilChemistryMeTrX::MeTrX_spinup
lerr_t MeTrX_spinup()
Definition: soilchemistry-metrx-spinup.cpp:68
ldndc::SoilChemistryMeTrX::MeTrX_groundwater_access
void MeTrX_groundwater_access()
Definition: soilchemistry-metrx-transport.cpp:538
ldndc::SoilChemistryMeTrX::MeTrX_nitrogen_fertilizer_release
lerr_t MeTrX_nitrogen_fertilizer_release()
Transforms nitrogen from slow release nitrogen fertilizer to nh4.
Definition: soilchemistry-metrx-management.cpp:907
ldndc::SoilChemistryMeTrX::MeTrX_till
lerr_t MeTrX_till()
Definition: soilchemistry-metrx-management.cpp:699
ldndc::SoilChemistryMeTrX::MeTrX_freeze_thaw
lerr_t MeTrX_freeze_thaw()
Definition: soilchemistry-metrx-physics-chemistry.cpp:390
ldndc::SoilChemistryMeTrX::MeTrX_physics
lerr_t MeTrX_physics()
Definition: soilchemistry-metrx-physics-chemistry.cpp:155
ldndc::SoilChemistryMeTrX::MeTrX_pH_calculation
void MeTrX_pH_calculation()
Definition: soilchemistry-metrx-physics-chemistry.cpp:538
ldndc::SoilChemistryMeTrX::MeTrX_write_rates
lerr_t MeTrX_write_rates()
Definition: soilchemistry-metrx-integrate.cpp:19
ldndc::SoilChemistryMeTrX::MeTrX_fertilize
lerr_t MeTrX_fertilize()
Definition: soilchemistry-metrx-management.cpp:32
ldndc::SoilChemistryMeTrX::MeTrX_soil_organic_matter_turnover
void MeTrX_soil_organic_matter_turnover()
ldndc::SoilChemistryMeTrX::MeTrX_nh3_nh4_equilibrium
void MeTrX_nh3_nh4_equilibrium()
Definition: soilchemistry-metrx-physics-chemistry.cpp:32
ldndc::SoilChemistryMeTrX::MeTrX_leaching
void MeTrX_leaching()
Downwards transport of solutes, litter and humus with percolation water.
Definition: soilchemistry-metrx-transport.cpp:24
ldndc::SoilChemistryMeTrX::MeTrX_urea_hydrolysis
void MeTrX_urea_hydrolysis()
Definition: soilchemistry-metrx-management.cpp:857
ldndc::SoilChemistryMeTrX::MeTrX_pertubation
lerr_t MeTrX_pertubation()
Definition: soilchemistry-metrx-transport.cpp:1352
ldndc::SoilChemistryMeTrX::MeTrX_fragmentation
lerr_t MeTrX_fragmentation()
Definition: soilchemistry-metrx-fragmentation.cpp:24
ldndc::SoilChemistryMeTrX::MeTrX_plant_respiration
lerr_t MeTrX_plant_respiration(size_t)
Updates o2 and co2 concentrations in soil layers. There is no o2 mass conservation guaranteed because...
Definition: soilchemistry-metrx-management.cpp:1000
ldndc::SoilChemistryMeTrX::MeTrX_manure
lerr_t MeTrX_manure()
Definition: soilchemistry-metrx-management.cpp:261
ldndc::SoilChemistryMeTrX::MeTrX_write_output
lerr_t MeTrX_write_output()
Definition: soilchemistry-metrx-output.cpp:16
ldndc::SoilChemistryMeTrX::MeTrX_reset
lerr_t MeTrX_reset()
Definition: soilchemistry-metrx-reset.cpp:36
ldndc::SoilChemistryMeTrX::MeTrX_check_for_negative_value
lerr_t MeTrX_check_for_negative_value(char const *)
iterates over complete soilchemistry state and checks for negative values
Definition: soilchemistry-metrx-balance-check.cpp:174
ldndc::SoilChemistryMeTrX::MeTrX_metabolism
lerr_t MeTrX_metabolism()
Definition: soilchemistry-metrx-microbial-dynamics.cpp:187
ldndc::SoilChemistryMeTrX::MeTrX_clay_nh4_equilibrium
void MeTrX_clay_nh4_equilibrium()
Definition: soilchemistry-metrx-physics-chemistry.cpp:94
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Member Data Documentation

◆ N_MINERALISATION_FRACTION

const double ldndc::SoilChemistryMeTrX::N_MINERALISATION_FRACTION = 0.5
staticprivate

Fractionation factor determining the share of decomposed nitrogen from different sources being mineralized to NH4 [-]

◆ TNORM

const double ldndc::SoilChemistryMeTrX::TNORM = 293.2
staticprivate

Reference temperature [K]

Referenced by MeTrX_physics().