R/decomp.R
In PNNL-TES/millenial:
#' Decomposition
#'
#' @param forc_st Soil temperature (K)
#' @param forc_sw Soil moisture (fraction)
#' @param psi Soil water potential at saturation (MPa)
#' @param forc_npp forc_npp
#' @param forc_roots forc_roots
#' @param forc_exoenzyme forc_exoenzyme
#' @param clay Clay (fraction)
#' @param LMWC Low molecular weight C (i.e., root exudates and the by-products of exoenzyme activity)
#' @param POM particulate organic matter (i.e., free fragments of plant detritus)
#' @param MB Microbial biomass C
#' @param MINERAL Mineral-associated organic matter
#' @param SOILAGG Aggregate C
#' @param globals List of global variables
#'
#' @return A list containing LMWC, POM, MB, MINERAL,
#' SOILAGG, f_LM_leaching, f_MI_LM_des, f_LM_MI_sor, f_LM_MB_uptake,
#' f_PO_LM_dep, f_MB_MI_sor, f_PO_SO_agg, f_MI_SO_agg,
#' f_SO_PO_break, f_SO_MI_break, and f_MB_atm.
#' @export
decomp <- function(forc_st, forc_sw, psi, forc_npp, forc_roots,
forc_exoenzyme, clay, LMWC, POM, MB, MINERAL,
SOILAGG, klmc, kes, k_leaching, CUEref, CUET, Taeref,
Vpom_lmc, kpom, kmic, Vpom_agg, kpom_agg, AGGmax,
Vmin_agg, kmin_agg, kagg, M_Lmin, Vm_l, km_l) {
# 537 ! decomposition subroutine start
# 538 subroutine decomp(forc_st, forc_sw, psi, forc_npp, forc_roots, &
# 539 forc_exoenzyme, clay, LMWC, POM, MB, MINERAL, SOILAGG, f_LM_leaching, f_MI_LM_des,&
# 540 f_LM_MI_sor, f_LM_MB_uptake,f_PO_LM_dep, f_MB_MI_sor,f_PO_SO_agg, f_MI_SO_agg,&
# 541 f_SO_PO_break, f_SO_MI_break, f_MB_atm)
# 542
# 543 implicit none
# 544 integer,parameter :: r8 = selected_real_kind(12) ! 8 byte real
# 545 integer,parameter :: r6 = selected_real_kind(8) ! 8 byte real
# 546 real(r8), intent(in) :: forc_st ! soil temperature (Kelvin) (-nlevsno+1:nlevgrnd)
# 547 real(r8), intent(in) :: forc_sw ! soil moisture (fraction)
# 548 real(r8), intent(in) :: psi ! soil water potential at saturation for CN code (MPa)
# 549 real(r8), intent(in) :: forc_npp
# 550 real(r8), intent(in) :: forc_roots
# 551 ! real(r8), intent(in) :: pH
# 552
# 553 real(r8),intent(inout) :: forc_exoenzyme
# 554 real, intent(inout) :: clay
# 555 real(r8),intent(inout) :: LMWC
# 556 real(r8),intent(inout) :: POM
# 557 real(r8),intent(inout) :: MB
# 558 real(r8),intent(inout) :: MINERAL
# 559 real(r8),intent(inout) :: SOILAGG
# 560 real(r8),intent(inout) :: f_LM_leaching
# 561 real(r8),intent(inout) :: f_MI_LM_des
# 562 real(r8),intent(inout) :: f_LM_MI_sor
# 563 real(r8),intent(inout) :: f_LM_MB_uptake
# 564 real(r8),intent(inout) :: f_PO_LM_dep
# 565 real(r8),intent(inout) :: f_MB_MI_sor
# 566 real(r8),intent(inout) :: f_PO_SO_agg
# 567 real(r8),intent(inout) :: f_MI_SO_agg
# 568 real(r8),intent(inout) :: f_SO_PO_break
# 569 real(r8),intent(inout) :: f_SO_MI_break
# 570 real(r8),intent(inout) :: f_MB_atm
# 571
# 572 real(r8) :: k_leaching
# 573 real(r8) :: Vm_l
# 574 real(r8) :: km_l
# 575 real(r8) :: M_Lmin
# 576 real(r8) :: klmc_min
# 577 real(r8) :: Qmax
# 578 real(r8) :: klmc
# 579 real(r8) :: kes
# 580 real(r8) :: CUEref
# 581 real(r8) :: CUET
# 582 real(r8) :: Taeref
# 583 real(r8) :: Vpom_lmc
# 584 real(r8) :: kpom
# 585 real(r8) :: k_POMes
# 586 real(r8) :: kmic_min
# 587 real(r8) :: kmic
# 588 real(r8) :: Vpom_agg
# 589 real(r8) :: kpom_agg
# 590 real(r8) :: Vmin_agg
# 591 real(r8) :: kmin_agg
# 592 real(r8) :: AGGmax
# 593 real(r8) :: kagg
# 594
# 595 ! local pointers to implicit out scalars
# 596 !
# 597 ! !OTHER LOCAL VARIABLES:
# 598
# 599 real :: temp, temp2, temp3 ! temporary variables
# 600 real :: psi_tem1, psi_tem2
# 601 real :: k_sorption ! temporar variable for k of sorption
# 602 ! real :: Qmax ! maximum sorption capacity mg / kg (mayes et al, 2012, SSSAJ)
# 603 real(r8) :: t_scalar ! soil temperature scalar for decomp
# 604 real(r8) :: t_scalar_mb ! soil temperature scalar for decomp
# 605 real(r8) :: minpsi, maxpsi ! limits for soil water scalar for decomp
# 606 ! real :: psi ! temporary soilpsi for water scalar
# 607 real :: w_scalar ! soil water scalar for decomp
# 608 real :: rate_scalar ! combined rate scalar for decomp
# 609 real :: pH
# 610 real :: f_SO_break
# 611 real(r8) :: t_scalar_reverse ! soil temperature scalar for decomp
# 612 real(r8) :: w_scalar_reverse ! soil temperature scalar for decomp
# 613
# 614 !~ !-----------------------------------------------------------------------
# 615
# 616 common /global/ &
# 617 k_leaching, &
# 618 Vm_l, &
# 619 km_l, &
# 620 M_Lmin, &
# 621 klmc_min, &
# 622 Qmax, &
# 623 klmc, &
# 624 kes, &
# 625 CUEref, &
# 626 CUET, &
# 627 Taeref, &
# 628 Vpom_lmc, &
# 629 kpom, &
# 630 k_POMes, &
# 631 kmic_min, &
# 632 kmic, &
# 633 Vpom_agg, &
# 634 kpom_agg, &
# 635 Vmin_agg, &
# 636 kmin_agg, &
# 637 AGGmax, &
# 638 kagg
# 639
# 640 t_scalar = 0._r8
# 641 t_scalar_reverse = 0._r8
# 642 temp = (forc_st - 15._r8) / 10._r8
# 643 t_scalar = t_scalar + 2. **(temp)
# 644 t_scalar_reverse = t_scalar_reverse + 0.5**(temp)
temp <- (forc_st - 15) / 10
t_scalar <- 2 ^ temp
t_scalar_reverse <- 0.5 ^ temp
# 645
# 646 t_scalar_mb = 0._r8
# 647 temp = (forc_st - 15._r8) / 10._r8
# 648 t_scalar_mb = t_scalar_mb + 2.**(temp)
t_scalar_mb <- 2 ^ temp
# 649
# 650 ! print *, "t_scalar", t_scalar, minpsi, maxpsi, psi
# 651 minpsi = -10.0_r8
# 652 w_scalar = 0._r8
# 653 maxpsi = -0.01_r8
# 654 pH = 7.0
minpsi <- -10
w_scalar <- 0
maxpsi <- -0.01
pH <- 7
# 655 !~ ! print *, " here ", minpsi / psi, minpsi / maxpsi
# 656 !~ psi_tem1 = minpsi / psi
# 657 !~ psi_tem2 = minpsi / maxpsi
# 658 !~ if (psi > maxpsi) then
# 659 !~ w_scalar = 1.
# 660 !~ end if
# 661 !~ if (psi < minpsi) then
# 662 !~ w_scalar = 0.
# 663 !~ else
# 664 !~ w_scalar = w_scalar + log(psi_tem1) / log(psi_tem2) * 2.3
# 665 !~ ! w_scalar = w_scalar + (log(1.0 * minpsi/psi))!/log(1.0 * minpsi/maxpsi))
# 666 !~ end if
# 667
# 668 ! xiaofeng replaced above codes with following
# 669 if (psi > minpsi) then
# 670 w_scalar = w_scalar + (psi-minpsi)*(psi-maxpsi)/((psi-minpsi)*(psi-maxpsi) - &
# 671 (psi-(maxpsi-(maxpsi-minpsi)/3.))*(psi-(maxpsi-(maxpsi-minpsi)/3.)))
# 672 end if
if (psi > minpsi) {
w_scalar = w_scalar + (psi - minpsi) * (psi - maxpsi) /
((psi - minpsi) * (psi - maxpsi) - (psi - (maxpsi - (maxpsi - minpsi) / 3)) *
(psi- (maxpsi - (maxpsi - minpsi) / 3)))
}
# 673 w_scalar = w_scalar ** 0.5
w_scalar <- sqrt(w_scalar)
# 674 ! print *, "w_scalar", w_scalar
# 675
# 676 !#century temperature function
# 677 !soilTemp <- seq(-20,40,length.out = 100)
# 678 !teff <- c(15.4, 11.75, 29.7, 0.031)
# 679 !tfunc <- (teff[2] + (teff[3]/pi)* atan(pi*teff[4]*(soilTemp - teff[1]))) / (teff[2] + (teff[3]/pi)* atan(pi*teff[4]*(30 - teff[1])))
# 680 t_scalar = (11.75 + (29.7 / 3.1415926) * ATAN(real(3.1415926*0.031*(forc_st - 15.4)))) / &
# 681 (11.75 + (29.7 / 3.1415926) * ATAN(real(3.1415926 * 0.031 *(30.0 - 15.4))))
# Equation 3 in Abramoff et al. (2017)
t_scalar <- (11.75 + (29.7 / pi) * atan(pi * 0.031 * (forc_st - 15.4))) /
(11.75 + (29.7 / pi) * atan(pi * 0.031 *(30.0 - 15.4)))
# 682 t_scalar_mb = t_scalar
t_scalar_mb <- t_scalar
# 683
# 684 !#century water function
# 685 !relwc <- seq(0,1,length.out = 100)
# 686 !wfunc <- 1/(1 + 30 * exp(-9*relwc))
# 687 w_scalar = 1.0 / (1.0 + 30. * EXP(real(-9.0 * forc_sw)))
w_scalar <- 1.0 / (1.0 + 30 * exp(-9.0 * forc_sw))
# 688
# 689 ! LMWC -> out of sysem LWMMWC leaching
# 690 if (LMWC > 0._r8) then
# 691 f_LM_leaching = LMWC * k_leaching * t_scalar !* w_scalar ! Xiaofeng removed water impact, after review at GBC June,2017
# 692 end if
# LMWC -> out of sysem LWMMWC leaching
# Equation 8 in Abramoff et al. (2017) except Xiaofeng removed water impact after review at GBC, June 2017
f_LM_leaching <- LMWC * k_leaching * t_scalar #* w_scalar ! Xiaofeng removed water impact, after review at GBC June,2017
# 693
# 694 !~ ! MINERAL -> LWMC desorption Xu found this processes is not imporant as we treat below desorption function as double way, blocked it
# 695 !~ if (MINERAL > M_Lmin) then
# 696 !~ f_MI_LM_des = Vm_l * (MINERAL - M_Lmin) / (km_l + MINERAL - M_Lmin) * t_scalar * w_scalar
# 697 !~ else
# 698 !~ f_MI_LM_des = 0.
# 699 !~ end if
if (MINERAL > M_Lmin) {
f_MI_LM_des <- Vm_l * (MINERAL - M_Lmin) / (km_l + MINERAL - M_Lmin) * t_scalar * w_scalar
} else {
f_MI_LM_des <- 0
}
# 700
# 701 ! LMWC -> MINERAL: This desorption function is from Mayes 2012, SSAJ
# 702 klmc_min = (10.0 ** (-0.186 * pH - 0.216)) / 24.0
# LMWC -> MINERAL: This desorption function is from Mayes 2012, SSAJ
klmc_min <- (10.0 ^ (-0.186 * pH - 0.216)) / 24.0
# 703 ! Qmax = 10.0 ** (0.4833 * log(clay * 100.0) + 2.3282) * 1.35 ! 1.35 is bulk density to convert Q from mg/kg to mg/m3
# 704 Qmax = 10.0 ** (0.297 * log(clay * 100.0) + 2.355 + 0.50) !* 1.25 ! 1.35 is bulk density to convert Q from mg/kg to g/m2
# Equation 11 in Abramoff et al. (2017)
# "Qmax is the maximum sorption capacity (mg C kg-1 dry soil) and is converted to
# C density (g C m-2) by multiplying soil bulk density (BD = 1350 kg m-3), assuming
# a 1 m soil profile. The parameters c1 and c2 are the coefficients for computing
# Qmax from the clay content in percent, derived from Mayes et al. (2012)."
# 2019-03-09 note: per Xiaofeng Xu, they ended up using 1.0 for bulk density
Qmax <- 10.0 ^ (0.297 * log(clay * 100.0) + 2.355 + 0.50) * 1.0
# 705 ! write(*,*)"Qmax: ", Qmax
# 706 temp = (klmc_min * Qmax * LMWC ) / (2. + klmc_min * LMWC) - MINERAL
temp <- (klmc_min * Qmax * LMWC ) / (2 + klmc_min * LMWC) - MINERAL
# 707 ! if(temp > 0)then
# 708 f_LM_MI_sor = (temp / Qmax + 0.0015) * LMWC / 50. * t_scalar * w_scalar !* t_scalar * w_scalar !* (LMWC / 200) * (LMWC / 200)
f_LM_MI_sor <- (temp / Qmax + 0.0015) * LMWC / 50 * t_scalar * w_scalar #* t_scalar * w_scalar !* (LMWC / 200) * (LMWC / 200)
# 709 ! else
# 710 ! f_LM_MI_sor = 0.
# 711 ! end if
# 712 ! f_LM_MI_sor = temp / (Qmax - MINERAL) * LMWC / 50. !* t_scalar * w_scalar !* (LMWC / 200) * (LMWC / 200)
# 713
# 714 if (f_LM_MI_sor < (LMWC * 0.9)) then
# 715 f_LM_MI_sor = f_LM_MI_sor
# 716 else
# 717 f_LM_MI_sor = LMWC * 0.9
# 718 end if
if (f_LM_MI_sor < (LMWC * 0.9)) {
f_LM_MI_sor <- f_LM_MI_sor
} else {
f_LM_MI_sor <- LMWC * 0.9
}
# 719
# 720 !~ if(f_LM_MI_sor < 0) then
# 721 !~ f_LM_MI_sor = 0.
# 722 !~ end if
# 723
# 724 ! print *, klmc_min, Qmax, f_LM_MI_sor, LMWC, MINERAL
# 725
# 726 ! LMWC -> MB
# 727 if (LMWC > 0._r8) then
# 728 f_LM_MB_uptake = LMWC * klmc * t_scalar * w_scalar * MB / (MB + kes) * LMWC / (20. + LMWC)
# 729 temp2 = f_LM_MB_uptake * (1. - (CUEref + CUET * (forc_st - Taeref)))
# 730 if(temp2 < 0._r8) then
# 731 temp2 = 0_r8
# 732 end if
# 733 f_LM_MB_uptake = f_LM_MB_uptake - temp2
# 734 end if
# LMWC -> MB
f_LM_MB_uptake <- LMWC * klmc * t_scalar * w_scalar * MB / (MB + kes) * LMWC / (20 + LMWC)
temp2 <- f_LM_MB_uptake * (1 - (CUEref + CUET * (forc_st - Taeref)))
temp2 <- max(temp2, 0)
f_LM_MB_uptake <- f_LM_MB_uptake - temp2
# 735
# 736 ! POM -> LMWC
# 737 if (POM > 0._r8) then
# 738 f_PO_LM_dep = Vpom_lmc * POM / (POM + kpom) * t_scalar * w_scalar !* (1. - MB / (MB + k_POMes))
# 739 end if
# POM -> LMWC
# "Decomposition of POM is governed by a double Michaelis–Menten equation,
# where Vpl is the maximum rate of POM decomposition, Kpl is the half-
# saturation constant, B is the microbial biomass carbon, and Kpe is the
# half-saturation constant of microbial control on POM mineralization.
# Equation 2 in Abramoff et al. (2017)
f_PO_LM_dep <- Vpom_lmc * POM / (POM + kpom) * t_scalar * w_scalar #* (1. - MB / (MB + k_POMes))
# 740
# 741 if(f_PO_LM_dep > (0.9 * POM)) then
# 742 f_PO_LM_dep = 0.9 * POM
# 743 end if
f_PO_LM_dep <- max(f_PO_LM_dep, 0.9 * POM)
# 744
# 745 ! print *, f_PO_LM_dep, Vpom_lmc, POM, kpom, MB, k_POMes
# 746
# 747 ! MB -> MINERAL
# 748 !~ if (MB > 0._r8) then
# 749 !~ temp = kmic_min * Qmax * MB / (1.0 + kmic_min * MB) - MINERAL
# 750 !~ f_MB_MI_sor = temp / Qmax * MB / 50. * t_scalar * w_scalar !* (MB / 200) * (MB / 200)
# 751 !~ end if
# 752
# 753 if (MB > 0._r8 .and. MINERAL < Qmax) then
# 754 f_MB_MI_sor = MB * kmic * 0.15 * t_scalar_mb * w_scalar !* (MB / 200) * (MB / 200)
# 755 else
# 756 f_MB_MI_sor = 0.
# 757 end if
if (MB > 0 & MINERAL < Qmax) {
f_MB_MI_sor <- MB * kmic * 0.15 * t_scalar_mb * w_scalar #* (MB / 200) * (MB / 200)
} else {
f_MB_MI_sor <- 0
}
# 758
# 759 if(f_MB_MI_sor > 0.9 * MB) then
# 760 f_MB_MI_sor = 0.9 * MB
# 761 end if
f_MB_MI_sor <- max(f_MB_MI_sor, 0.9 * MB)
# 762 if(f_MB_MI_sor < 0.) then
# 763 f_MB_MI_sor = 0.
# 764 end if
f_MB_MI_sor <- max(f_MB_MI_sor, 0)
# 765
# 766 ! MB -> ATM
# 767 if (MB > 0._r8) then
# 768 f_MB_atm = temp2 + MB * kmic * t_scalar_mb * w_scalar
# 769 end if
# MB -> ATM
f_MB_atm <- temp2 + MB * kmic * t_scalar_mb * w_scalar
# 770
# 771 ! POM -> SOILAGG
# 772 if (POM > 0._r8) then
# 773 f_PO_SO_agg = Vpom_agg * POM / (kpom_agg + POM) * (1. - SOILAGG / AGGmax) * t_scalar * w_scalar
# 774 end if
# POM -> SOILAGG
# "The formation of aggregate C (A) from POM follows Michaelis–Menten dynamics,
# where Vpa is the maximum rate of aggregate formation, Kpa is the half-
# saturation constant of aggregate formation, and Amax is the maximum capacity
# of C in soil aggregates.
# Eauation 5 in Abramoff et al. (2017)
f_PO_SO_agg <- Vpom_agg * POM / (kpom_agg + POM) * (1 - SOILAGG / AGGmax) * t_scalar * w_scalar
# 775
# 776 if(f_PO_SO_agg > 0.9 * POM) then
# 777 f_PO_SO_agg = 0.9 * POM
# 778 end if
f_PO_SO_agg <- max(f_PO_SO_agg, 0.9 * POM)
# 779
# 780 ! print *, "POM > soilAGG: ", f_PO_SO_agg, Vpom_agg, POM, kpom_agg, SOILAGG, AGGmax
# 781
# 782 ! MINERAL -> SOILAGG
# 783 if (MINERAL > 0._r8) then
# 784 f_MI_SO_agg = Vmin_agg * MINERAL / (kmin_agg + MINERAL) * (1. - SOILAGG / AGGmax) !* t_scalar * w_scalar
# 785 end if
# MINERAL -> SOILAGG
f_MI_SO_agg <- Vmin_agg * MINERAL / (kmin_agg + MINERAL) * (1 - SOILAGG / AGGmax) #* t_scalar * w_scalar
# 786
# 787 if(f_MI_SO_agg>0.9 * MINERAL) then
# 788 f_MI_SO_agg = 0.9 * MINERAL
# 789 end if
f_MI_SO_agg <- max(f_MI_SO_agg, 0.9 * MINERAL)
# 790
# 791 ! SOILAGG -> MINERAL
# 792 if (SOILAGG > 0._r8) then
# 793 f_SO_break = SOILAGG * kagg * t_scalar * w_scalar
# 794 f_SO_PO_break = f_SO_break * 1.5 / 3.
# 795 f_SO_MI_break = f_SO_break * 1.5 / 3.
# 796 end if
# SOILAGG -> MINERAL
# Soil aggregate C breakdown is partitioned to POM and MAOM,
# where kb is the rate of breakdown.
# Eauation 6 in Abramoff et al. (2017)
f_SO_break <- SOILAGG * kagg * t_scalar * w_scalar
f_SO_PO_break <- f_SO_break * 1.5 / 3
f_SO_MI_break <- f_SO_break * 1.5 / 3
# 797
# 798 ! print *, "before update:", forc_npp, LMWC,POM,MB,MINERAL,SOILAGG,f_PO_LM_dep,f_MI_LM_des,f_LM_leaching,f_LM_MI_sor,f_LM_MB_uptake,&
# 799 ! f_SO_PO_break,f_PO_LM_dep,f_PO_SO_agg
# 800
# 801 if((f_PO_LM_dep + f_PO_SO_agg) > POM) then
# 802 temp3 = POM / (f_PO_LM_dep + f_PO_SO_agg)
# 803 f_PO_LM_dep = f_PO_LM_dep * temp3
# 804 f_PO_SO_agg = f_PO_SO_agg * temp3
# 805 end if
if((f_PO_LM_dep + f_PO_SO_agg) > POM) {
temp3 <- POM / (f_PO_LM_dep + f_PO_SO_agg)
f_PO_LM_dep <- f_PO_LM_dep * temp3
f_PO_SO_agg <- f_PO_SO_agg * temp3
}
# 806
# 807 LMWC = LMWC + (f_PO_LM_dep + f_MI_LM_des - f_LM_leaching - f_LM_MI_sor - f_LM_MB_uptake - temp2) + forc_npp / 3.
# Update state variables
# Equation 7 in Abramoff et al. (2017)
LMWC <- LMWC + (f_PO_LM_dep + f_MI_LM_des - f_LM_leaching - f_LM_MI_sor - f_LM_MB_uptake - temp2) + forc_npp / 3
# 808
# 809 POM = POM + (f_SO_PO_break - f_PO_LM_dep - f_PO_SO_agg) + forc_npp * 2. / 3.
# Equation 1 in Abramoff et al. (2017)
POM <- POM + (f_SO_PO_break - f_PO_LM_dep - f_PO_SO_agg) + forc_npp * 2 / 3
# 810
# 811 MB = MB + (f_LM_MB_uptake - f_MB_MI_sor - f_MB_atm)
MB <- MB + (f_LM_MB_uptake - f_MB_MI_sor - f_MB_atm)
# 812
# 813 ! print *, "MB, LM_MB, MB_Mi, MB_ATM", MB, f_LM_MB_uptake, f_MB_MI_sor, f_MB_atm
# 814
# 815 MINERAL = MINERAL + (f_LM_MI_sor + f_MB_MI_sor + f_SO_MI_break - f_MI_LM_des - f_MI_SO_agg)
MINERAL <- MINERAL + (f_LM_MI_sor + f_MB_MI_sor + f_SO_MI_break - f_MI_LM_des - f_MI_SO_agg)
# 816
# 817 SOILAGG = SOILAGG + (f_PO_SO_agg + f_MI_SO_agg - f_SO_PO_break - f_SO_MI_break)
SOILAGG <- SOILAGG + (f_PO_SO_agg + f_MI_SO_agg - f_SO_PO_break - f_SO_MI_break)
# 818
# 819 ! print *, "after update:", LMWC,POM,MB,MINERAL,SOILAGG,f_PO_LM_dep,f_MI_LM_des,f_LM_leaching,f_LM_MI_sor,f_LM_MB_uptake,&
# 820 ! f_SO_PO_break,f_PO_LM_dep,f_PO_SO_agg
# 821
# 822 end subroutine decomp
# 823 ! decomposition subroutine end
list(LMWC = LMWC, POM = POM, MB = MB, MINERAL = MINERAL, SOILAGG = SOILAGG,
f_LM_leaching = f_LM_leaching, f_MI_LM_des = f_MI_LM_des,
f_LM_MI_sor = f_LM_MI_sor, f_LM_MB_uptake = f_LM_MB_uptake,
f_PO_LM_dep = f_PO_LM_dep, f_MB_MI_sor = f_MB_MI_sor,
f_PO_SO_agg = f_PO_SO_agg, f_MI_SO_agg = f_MI_SO_agg,
f_SO_PO_break = f_SO_PO_break, f_SO_MI_break = f_SO_MI_break,
f_MB_atm = f_MB_atm)
}
PNNL-TES/millenial documentation built on May 8, 2019, 8:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Decomposition
#'
#' @param forc_st Soil temperature (K)
#' @param forc_sw Soil moisture (fraction)
#' @param psi Soil water potential at saturation (MPa)
#' @param forc_npp forc_npp
#' @param forc_roots forc_roots
#' @param forc_exoenzyme forc_exoenzyme
#' @param clay Clay (fraction)
#' @param LMWC Low molecular weight C (i.e., root exudates and the by-products of exoenzyme activity)
#' @param POM particulate organic matter (i.e., free fragments of plant detritus)
#' @param MB Microbial biomass C
#' @param MINERAL Mineral-associated organic matter
#' @param SOILAGG Aggregate C
#' @param globals List of global variables
#'
#' @return A list containing LMWC, POM, MB, MINERAL,
#' SOILAGG, f_LM_leaching, f_MI_LM_des, f_LM_MI_sor, f_LM_MB_uptake,
#' f_PO_LM_dep, f_MB_MI_sor, f_PO_SO_agg, f_MI_SO_agg,
#' f_SO_PO_break, f_SO_MI_break, and f_MB_atm.
#' @export
decomp <- function(forc_st, forc_sw, psi, forc_npp, forc_roots,
forc_exoenzyme, clay, LMWC, POM, MB, MINERAL,
SOILAGG, klmc, kes, k_leaching, CUEref, CUET, Taeref,
Vpom_lmc, kpom, kmic, Vpom_agg, kpom_agg, AGGmax,
Vmin_agg, kmin_agg, kagg, M_Lmin, Vm_l, km_l) {
# 537 ! decomposition subroutine start
# 538 subroutine decomp(forc_st, forc_sw, psi, forc_npp, forc_roots, &
# 539 forc_exoenzyme, clay, LMWC, POM, MB, MINERAL, SOILAGG, f_LM_leaching, f_MI_LM_des,&
# 540 f_LM_MI_sor, f_LM_MB_uptake,f_PO_LM_dep, f_MB_MI_sor,f_PO_SO_agg, f_MI_SO_agg,&
# 541 f_SO_PO_break, f_SO_MI_break, f_MB_atm)
# 542
# 543 implicit none
# 544 integer,parameter :: r8 = selected_real_kind(12) ! 8 byte real
# 545 integer,parameter :: r6 = selected_real_kind(8) ! 8 byte real
# 546 real(r8), intent(in) :: forc_st ! soil temperature (Kelvin) (-nlevsno+1:nlevgrnd)
# 547 real(r8), intent(in) :: forc_sw ! soil moisture (fraction)
# 548 real(r8), intent(in) :: psi ! soil water potential at saturation for CN code (MPa)
# 549 real(r8), intent(in) :: forc_npp
# 550 real(r8), intent(in) :: forc_roots
# 551 ! real(r8), intent(in) :: pH
# 552
# 553 real(r8),intent(inout) :: forc_exoenzyme
# 554 real, intent(inout) :: clay
# 555 real(r8),intent(inout) :: LMWC
# 556 real(r8),intent(inout) :: POM
# 557 real(r8),intent(inout) :: MB
# 558 real(r8),intent(inout) :: MINERAL
# 559 real(r8),intent(inout) :: SOILAGG
# 560 real(r8),intent(inout) :: f_LM_leaching
# 561 real(r8),intent(inout) :: f_MI_LM_des
# 562 real(r8),intent(inout) :: f_LM_MI_sor
# 563 real(r8),intent(inout) :: f_LM_MB_uptake
# 564 real(r8),intent(inout) :: f_PO_LM_dep
# 565 real(r8),intent(inout) :: f_MB_MI_sor
# 566 real(r8),intent(inout) :: f_PO_SO_agg
# 567 real(r8),intent(inout) :: f_MI_SO_agg
# 568 real(r8),intent(inout) :: f_SO_PO_break
# 569 real(r8),intent(inout) :: f_SO_MI_break
# 570 real(r8),intent(inout) :: f_MB_atm
# 571
# 572 real(r8) :: k_leaching
# 573 real(r8) :: Vm_l
# 574 real(r8) :: km_l
# 575 real(r8) :: M_Lmin
# 576 real(r8) :: klmc_min
# 577 real(r8) :: Qmax
# 578 real(r8) :: klmc
# 579 real(r8) :: kes
# 580 real(r8) :: CUEref
# 581 real(r8) :: CUET
# 582 real(r8) :: Taeref
# 583 real(r8) :: Vpom_lmc
# 584 real(r8) :: kpom
# 585 real(r8) :: k_POMes
# 586 real(r8) :: kmic_min
# 587 real(r8) :: kmic
# 588 real(r8) :: Vpom_agg
# 589 real(r8) :: kpom_agg
# 590 real(r8) :: Vmin_agg
# 591 real(r8) :: kmin_agg
# 592 real(r8) :: AGGmax
# 593 real(r8) :: kagg
# 594
# 595 ! local pointers to implicit out scalars
# 596 !
# 597 ! !OTHER LOCAL VARIABLES:
# 598
# 599 real :: temp, temp2, temp3 ! temporary variables
# 600 real :: psi_tem1, psi_tem2
# 601 real :: k_sorption ! temporar variable for k of sorption
# 602 ! real :: Qmax ! maximum sorption capacity mg / kg (mayes et al, 2012, SSSAJ)
# 603 real(r8) :: t_scalar ! soil temperature scalar for decomp
# 604 real(r8) :: t_scalar_mb ! soil temperature scalar for decomp
# 605 real(r8) :: minpsi, maxpsi ! limits for soil water scalar for decomp
# 606 ! real :: psi ! temporary soilpsi for water scalar
# 607 real :: w_scalar ! soil water scalar for decomp
# 608 real :: rate_scalar ! combined rate scalar for decomp
# 609 real :: pH
# 610 real :: f_SO_break
# 611 real(r8) :: t_scalar_reverse ! soil temperature scalar for decomp
# 612 real(r8) :: w_scalar_reverse ! soil temperature scalar for decomp
# 613
# 614 !~ !-----------------------------------------------------------------------
# 615
# 616 common /global/ &
# 617 k_leaching, &
# 618 Vm_l, &
# 619 km_l, &
# 620 M_Lmin, &
# 621 klmc_min, &
# 622 Qmax, &
# 623 klmc, &
# 624 kes, &
# 625 CUEref, &
# 626 CUET, &
# 627 Taeref, &
# 628 Vpom_lmc, &
# 629 kpom, &
# 630 k_POMes, &
# 631 kmic_min, &
# 632 kmic, &
# 633 Vpom_agg, &
# 634 kpom_agg, &
# 635 Vmin_agg, &
# 636 kmin_agg, &
# 637 AGGmax, &
# 638 kagg
# 639
# 640 t_scalar = 0._r8
# 641 t_scalar_reverse = 0._r8
# 642 temp = (forc_st - 15._r8) / 10._r8
# 643 t_scalar = t_scalar + 2. **(temp)
# 644 t_scalar_reverse = t_scalar_reverse + 0.5**(temp)
temp <- (forc_st - 15) / 10
t_scalar <- 2 ^ temp
t_scalar_reverse <- 0.5 ^ temp
# 645
# 646 t_scalar_mb = 0._r8
# 647 temp = (forc_st - 15._r8) / 10._r8
# 648 t_scalar_mb = t_scalar_mb + 2.**(temp)
t_scalar_mb <- 2 ^ temp
# 649
# 650 ! print *, "t_scalar", t_scalar, minpsi, maxpsi, psi
# 651 minpsi = -10.0_r8
# 652 w_scalar = 0._r8
# 653 maxpsi = -0.01_r8
# 654 pH = 7.0
minpsi <- -10
w_scalar <- 0
maxpsi <- -0.01
pH <- 7
# 655 !~ ! print *, " here ", minpsi / psi, minpsi / maxpsi
# 656 !~ psi_tem1 = minpsi / psi
# 657 !~ psi_tem2 = minpsi / maxpsi
# 658 !~ if (psi > maxpsi) then
# 659 !~ w_scalar = 1.
# 660 !~ end if
# 661 !~ if (psi < minpsi) then
# 662 !~ w_scalar = 0.
# 663 !~ else
# 664 !~ w_scalar = w_scalar + log(psi_tem1) / log(psi_tem2) * 2.3
# 665 !~ ! w_scalar = w_scalar + (log(1.0 * minpsi/psi))!/log(1.0 * minpsi/maxpsi))
# 666 !~ end if
# 667
# 668 ! xiaofeng replaced above codes with following
# 669 if (psi > minpsi) then
# 670 w_scalar = w_scalar + (psi-minpsi)*(psi-maxpsi)/((psi-minpsi)*(psi-maxpsi) - &
# 671 (psi-(maxpsi-(maxpsi-minpsi)/3.))*(psi-(maxpsi-(maxpsi-minpsi)/3.)))
# 672 end if
if (psi > minpsi) {
w_scalar = w_scalar + (psi - minpsi) * (psi - maxpsi) /
((psi - minpsi) * (psi - maxpsi) - (psi - (maxpsi - (maxpsi - minpsi) / 3)) *
(psi- (maxpsi - (maxpsi - minpsi) / 3)))
}
# 673 w_scalar = w_scalar ** 0.5
w_scalar <- sqrt(w_scalar)
# 674 ! print *, "w_scalar", w_scalar
# 675
# 676 !#century temperature function
# 677 !soilTemp <- seq(-20,40,length.out = 100)
# 678 !teff <- c(15.4, 11.75, 29.7, 0.031)
# 679 !tfunc <- (teff[2] + (teff[3]/pi)* atan(pi*teff[4]*(soilTemp - teff[1]))) / (teff[2] + (teff[3]/pi)* atan(pi*teff[4]*(30 - teff[1])))
# 680 t_scalar = (11.75 + (29.7 / 3.1415926) * ATAN(real(3.1415926*0.031*(forc_st - 15.4)))) / &
# 681 (11.75 + (29.7 / 3.1415926) * ATAN(real(3.1415926 * 0.031 *(30.0 - 15.4))))
# Equation 3 in Abramoff et al. (2017)
t_scalar <- (11.75 + (29.7 / pi) * atan(pi * 0.031 * (forc_st - 15.4))) /
(11.75 + (29.7 / pi) * atan(pi * 0.031 *(30.0 - 15.4)))
# 682 t_scalar_mb = t_scalar
t_scalar_mb <- t_scalar
# 683
# 684 !#century water function
# 685 !relwc <- seq(0,1,length.out = 100)
# 686 !wfunc <- 1/(1 + 30 * exp(-9*relwc))
# 687 w_scalar = 1.0 / (1.0 + 30. * EXP(real(-9.0 * forc_sw)))
w_scalar <- 1.0 / (1.0 + 30 * exp(-9.0 * forc_sw))
# 688
# 689 ! LMWC -> out of sysem LWMMWC leaching
# 690 if (LMWC > 0._r8) then
# 691 f_LM_leaching = LMWC * k_leaching * t_scalar !* w_scalar ! Xiaofeng removed water impact, after review at GBC June,2017
# 692 end if
# LMWC -> out of sysem LWMMWC leaching
# Equation 8 in Abramoff et al. (2017) except Xiaofeng removed water impact after review at GBC, June 2017
f_LM_leaching <- LMWC * k_leaching * t_scalar #* w_scalar ! Xiaofeng removed water impact, after review at GBC June,2017
# 693
# 694 !~ ! MINERAL -> LWMC desorption Xu found this processes is not imporant as we treat below desorption function as double way, blocked it
# 695 !~ if (MINERAL > M_Lmin) then
# 696 !~ f_MI_LM_des = Vm_l * (MINERAL - M_Lmin) / (km_l + MINERAL - M_Lmin) * t_scalar * w_scalar
# 697 !~ else
# 698 !~ f_MI_LM_des = 0.
# 699 !~ end if
if (MINERAL > M_Lmin) {
f_MI_LM_des <- Vm_l * (MINERAL - M_Lmin) / (km_l + MINERAL - M_Lmin) * t_scalar * w_scalar
} else {
f_MI_LM_des <- 0
}
# 700
# 701 ! LMWC -> MINERAL: This desorption function is from Mayes 2012, SSAJ
# 702 klmc_min = (10.0 ** (-0.186 * pH - 0.216)) / 24.0
# LMWC -> MINERAL: This desorption function is from Mayes 2012, SSAJ
klmc_min <- (10.0 ^ (-0.186 * pH - 0.216)) / 24.0
# 703 ! Qmax = 10.0 ** (0.4833 * log(clay * 100.0) + 2.3282) * 1.35 ! 1.35 is bulk density to convert Q from mg/kg to mg/m3
# 704 Qmax = 10.0 ** (0.297 * log(clay * 100.0) + 2.355 + 0.50) !* 1.25 ! 1.35 is bulk density to convert Q from mg/kg to g/m2
# Equation 11 in Abramoff et al. (2017)
# "Qmax is the maximum sorption capacity (mg C kg-1 dry soil) and is converted to
# C density (g C m-2) by multiplying soil bulk density (BD = 1350 kg m-3), assuming
# a 1 m soil profile. The parameters c1 and c2 are the coefficients for computing
# Qmax from the clay content in percent, derived from Mayes et al. (2012)."
# 2019-03-09 note: per Xiaofeng Xu, they ended up using 1.0 for bulk density
Qmax <- 10.0 ^ (0.297 * log(clay * 100.0) + 2.355 + 0.50) * 1.0
# 705 ! write(*,*)"Qmax: ", Qmax
# 706 temp = (klmc_min * Qmax * LMWC ) / (2. + klmc_min * LMWC) - MINERAL
temp <- (klmc_min * Qmax * LMWC ) / (2 + klmc_min * LMWC) - MINERAL
# 707 ! if(temp > 0)then
# 708 f_LM_MI_sor = (temp / Qmax + 0.0015) * LMWC / 50. * t_scalar * w_scalar !* t_scalar * w_scalar !* (LMWC / 200) * (LMWC / 200)
f_LM_MI_sor <- (temp / Qmax + 0.0015) * LMWC / 50 * t_scalar * w_scalar #* t_scalar * w_scalar !* (LMWC / 200) * (LMWC / 200)
# 709 ! else
# 710 ! f_LM_MI_sor = 0.
# 711 ! end if
# 712 ! f_LM_MI_sor = temp / (Qmax - MINERAL) * LMWC / 50. !* t_scalar * w_scalar !* (LMWC / 200) * (LMWC / 200)
# 713
# 714 if (f_LM_MI_sor < (LMWC * 0.9)) then
# 715 f_LM_MI_sor = f_LM_MI_sor
# 716 else
# 717 f_LM_MI_sor = LMWC * 0.9
# 718 end if
if (f_LM_MI_sor < (LMWC * 0.9)) {
f_LM_MI_sor <- f_LM_MI_sor
} else {
f_LM_MI_sor <- LMWC * 0.9
}
# 719
# 720 !~ if(f_LM_MI_sor < 0) then
# 721 !~ f_LM_MI_sor = 0.
# 722 !~ end if
# 723
# 724 ! print *, klmc_min, Qmax, f_LM_MI_sor, LMWC, MINERAL
# 725
# 726 ! LMWC -> MB
# 727 if (LMWC > 0._r8) then
# 728 f_LM_MB_uptake = LMWC * klmc * t_scalar * w_scalar * MB / (MB + kes) * LMWC / (20. + LMWC)
# 729 temp2 = f_LM_MB_uptake * (1. - (CUEref + CUET * (forc_st - Taeref)))
# 730 if(temp2 < 0._r8) then
# 731 temp2 = 0_r8
# 732 end if
# 733 f_LM_MB_uptake = f_LM_MB_uptake - temp2
# 734 end if
# LMWC -> MB
f_LM_MB_uptake <- LMWC * klmc * t_scalar * w_scalar * MB / (MB + kes) * LMWC / (20 + LMWC)
temp2 <- f_LM_MB_uptake * (1 - (CUEref + CUET * (forc_st - Taeref)))
temp2 <- max(temp2, 0)
f_LM_MB_uptake <- f_LM_MB_uptake - temp2
# 735
# 736 ! POM -> LMWC
# 737 if (POM > 0._r8) then
# 738 f_PO_LM_dep = Vpom_lmc * POM / (POM + kpom) * t_scalar * w_scalar !* (1. - MB / (MB + k_POMes))
# 739 end if
# POM -> LMWC
# "Decomposition of POM is governed by a double Michaelis–Menten equation,
# where Vpl is the maximum rate of POM decomposition, Kpl is the half-
# saturation constant, B is the microbial biomass carbon, and Kpe is the
# half-saturation constant of microbial control on POM mineralization.
# Equation 2 in Abramoff et al. (2017)
f_PO_LM_dep <- Vpom_lmc * POM / (POM + kpom) * t_scalar * w_scalar #* (1. - MB / (MB + k_POMes))
# 740
# 741 if(f_PO_LM_dep > (0.9 * POM)) then
# 742 f_PO_LM_dep = 0.9 * POM
# 743 end if
f_PO_LM_dep <- max(f_PO_LM_dep, 0.9 * POM)
# 744
# 745 ! print *, f_PO_LM_dep, Vpom_lmc, POM, kpom, MB, k_POMes
# 746
# 747 ! MB -> MINERAL
# 748 !~ if (MB > 0._r8) then
# 749 !~ temp = kmic_min * Qmax * MB / (1.0 + kmic_min * MB) - MINERAL
# 750 !~ f_MB_MI_sor = temp / Qmax * MB / 50. * t_scalar * w_scalar !* (MB / 200) * (MB / 200)
# 751 !~ end if
# 752
# 753 if (MB > 0._r8 .and. MINERAL < Qmax) then
# 754 f_MB_MI_sor = MB * kmic * 0.15 * t_scalar_mb * w_scalar !* (MB / 200) * (MB / 200)
# 755 else
# 756 f_MB_MI_sor = 0.
# 757 end if
if (MB > 0 & MINERAL < Qmax) {
f_MB_MI_sor <- MB * kmic * 0.15 * t_scalar_mb * w_scalar #* (MB / 200) * (MB / 200)
} else {
f_MB_MI_sor <- 0
}
# 758
# 759 if(f_MB_MI_sor > 0.9 * MB) then
# 760 f_MB_MI_sor = 0.9 * MB
# 761 end if
f_MB_MI_sor <- max(f_MB_MI_sor, 0.9 * MB)
# 762 if(f_MB_MI_sor < 0.) then
# 763 f_MB_MI_sor = 0.
# 764 end if
f_MB_MI_sor <- max(f_MB_MI_sor, 0)
# 765
# 766 ! MB -> ATM
# 767 if (MB > 0._r8) then
# 768 f_MB_atm = temp2 + MB * kmic * t_scalar_mb * w_scalar
# 769 end if
# MB -> ATM
f_MB_atm <- temp2 + MB * kmic * t_scalar_mb * w_scalar
# 770
# 771 ! POM -> SOILAGG
# 772 if (POM > 0._r8) then
# 773 f_PO_SO_agg = Vpom_agg * POM / (kpom_agg + POM) * (1. - SOILAGG / AGGmax) * t_scalar * w_scalar
# 774 end if
# POM -> SOILAGG
# "The formation of aggregate C (A) from POM follows Michaelis–Menten dynamics,
# where Vpa is the maximum rate of aggregate formation, Kpa is the half-
# saturation constant of aggregate formation, and Amax is the maximum capacity
# of C in soil aggregates.
# Eauation 5 in Abramoff et al. (2017)
f_PO_SO_agg <- Vpom_agg * POM / (kpom_agg + POM) * (1 - SOILAGG / AGGmax) * t_scalar * w_scalar
# 775
# 776 if(f_PO_SO_agg > 0.9 * POM) then
# 777 f_PO_SO_agg = 0.9 * POM
# 778 end if
f_PO_SO_agg <- max(f_PO_SO_agg, 0.9 * POM)
# 779
# 780 ! print *, "POM > soilAGG: ", f_PO_SO_agg, Vpom_agg, POM, kpom_agg, SOILAGG, AGGmax
# 781
# 782 ! MINERAL -> SOILAGG
# 783 if (MINERAL > 0._r8) then
# 784 f_MI_SO_agg = Vmin_agg * MINERAL / (kmin_agg + MINERAL) * (1. - SOILAGG / AGGmax) !* t_scalar * w_scalar
# 785 end if
# MINERAL -> SOILAGG
f_MI_SO_agg <- Vmin_agg * MINERAL / (kmin_agg + MINERAL) * (1 - SOILAGG / AGGmax) #* t_scalar * w_scalar
# 786
# 787 if(f_MI_SO_agg>0.9 * MINERAL) then
# 788 f_MI_SO_agg = 0.9 * MINERAL
# 789 end if
f_MI_SO_agg <- max(f_MI_SO_agg, 0.9 * MINERAL)
# 790
# 791 ! SOILAGG -> MINERAL
# 792 if (SOILAGG > 0._r8) then
# 793 f_SO_break = SOILAGG * kagg * t_scalar * w_scalar
# 794 f_SO_PO_break = f_SO_break * 1.5 / 3.
# 795 f_SO_MI_break = f_SO_break * 1.5 / 3.
# 796 end if
# SOILAGG -> MINERAL
# Soil aggregate C breakdown is partitioned to POM and MAOM,
# where kb is the rate of breakdown.
# Eauation 6 in Abramoff et al. (2017)
f_SO_break <- SOILAGG * kagg * t_scalar * w_scalar
f_SO_PO_break <- f_SO_break * 1.5 / 3
f_SO_MI_break <- f_SO_break * 1.5 / 3
# 797
# 798 ! print *, "before update:", forc_npp, LMWC,POM,MB,MINERAL,SOILAGG,f_PO_LM_dep,f_MI_LM_des,f_LM_leaching,f_LM_MI_sor,f_LM_MB_uptake,&
# 799 ! f_SO_PO_break,f_PO_LM_dep,f_PO_SO_agg
# 800
# 801 if((f_PO_LM_dep + f_PO_SO_agg) > POM) then
# 802 temp3 = POM / (f_PO_LM_dep + f_PO_SO_agg)
# 803 f_PO_LM_dep = f_PO_LM_dep * temp3
# 804 f_PO_SO_agg = f_PO_SO_agg * temp3
# 805 end if
if((f_PO_LM_dep + f_PO_SO_agg) > POM) {
temp3 <- POM / (f_PO_LM_dep + f_PO_SO_agg)
f_PO_LM_dep <- f_PO_LM_dep * temp3
f_PO_SO_agg <- f_PO_SO_agg * temp3
}
# 806
# 807 LMWC = LMWC + (f_PO_LM_dep + f_MI_LM_des - f_LM_leaching - f_LM_MI_sor - f_LM_MB_uptake - temp2) + forc_npp / 3.
# Update state variables
# Equation 7 in Abramoff et al. (2017)
LMWC <- LMWC + (f_PO_LM_dep + f_MI_LM_des - f_LM_leaching - f_LM_MI_sor - f_LM_MB_uptake - temp2) + forc_npp / 3
# 808
# 809 POM = POM + (f_SO_PO_break - f_PO_LM_dep - f_PO_SO_agg) + forc_npp * 2. / 3.
# Equation 1 in Abramoff et al. (2017)
POM <- POM + (f_SO_PO_break - f_PO_LM_dep - f_PO_SO_agg) + forc_npp * 2 / 3
# 810
# 811 MB = MB + (f_LM_MB_uptake - f_MB_MI_sor - f_MB_atm)
MB <- MB + (f_LM_MB_uptake - f_MB_MI_sor - f_MB_atm)
# 812
# 813 ! print *, "MB, LM_MB, MB_Mi, MB_ATM", MB, f_LM_MB_uptake, f_MB_MI_sor, f_MB_atm
# 814
# 815 MINERAL = MINERAL + (f_LM_MI_sor + f_MB_MI_sor + f_SO_MI_break - f_MI_LM_des - f_MI_SO_agg)
MINERAL <- MINERAL + (f_LM_MI_sor + f_MB_MI_sor + f_SO_MI_break - f_MI_LM_des - f_MI_SO_agg)
# 816
# 817 SOILAGG = SOILAGG + (f_PO_SO_agg + f_MI_SO_agg - f_SO_PO_break - f_SO_MI_break)
SOILAGG <- SOILAGG + (f_PO_SO_agg + f_MI_SO_agg - f_SO_PO_break - f_SO_MI_break)
# 818
# 819 ! print *, "after update:", LMWC,POM,MB,MINERAL,SOILAGG,f_PO_LM_dep,f_MI_LM_des,f_LM_leaching,f_LM_MI_sor,f_LM_MB_uptake,&
# 820 ! f_SO_PO_break,f_PO_LM_dep,f_PO_SO_agg
# 821
# 822 end subroutine decomp
# 823 ! decomposition subroutine end
list(LMWC = LMWC, POM = POM, MB = MB, MINERAL = MINERAL, SOILAGG = SOILAGG,
f_LM_leaching = f_LM_leaching, f_MI_LM_des = f_MI_LM_des,
f_LM_MI_sor = f_LM_MI_sor, f_LM_MB_uptake = f_LM_MB_uptake,
f_PO_LM_dep = f_PO_LM_dep, f_MB_MI_sor = f_MB_MI_sor,
f_PO_SO_agg = f_PO_SO_agg, f_MI_SO_agg = f_MI_SO_agg,
f_SO_PO_break = f_SO_PO_break, f_SO_MI_break = f_SO_MI_break,
f_MB_atm = f_MB_atm)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.