Pl: Normalization.Minerals

Calculation form Excel table. To 5 cations with optional Fe_p3_pfu calculation from charge balance.

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recalc.pl_nm <- function (wtp_data, ...) {

    #Names preparation
    ox_tnames <- c('SiO2',    'TiO2',     'Al2O3',     'Cr2O3',     'Fe2O3',     'FeO',       'MnO',     'MgO'    ,'CaO', 'BaO', 'Na2O', 'K2O');
    ox_names <-  c('SiO2_wtp','TiO2_wtp', 'Al2O3_wtp', 'Cr2O3_wtp', 'Fe2O3_wtp', 'FeO_wtp',   'MnO_wtp', 'MgO_wtp','CaO_wtp', 'BaO_wtp','Na2O_wtp','K2O_wtp');
    pfu_names <- c('Si_pfu',  'Ti_pfu',   'Al_pfu',    'Cr_pfu',    'Fe_p3_pfu', 'Fe_p2_pfu', 'Mn_pfu',  'Mg_pfu' ,'Ca_pfu','Ba_pfu', 'Na_pfu', 'K_pfu');

    #Periodic table load
    elem <- read.csv("constants_nmperiodic.csv",stringsAsFactors=F, dec = ".");
    tmelem <- data.frame(t(elem), stringsAsFactors = F);
    names(tmelem) <- elem$oxide;
    telem  <- selectNames(tmelem,ox_tnames);
    names(telem) <- ox_names;

    #Select columns
    wtp_group <- selectNames(wtp_data,ox_names);

    mole_cations <- rowApply('*', wtp_group, as.numeric(telem['ncations',]));
    mole_cations <- rowApply('/', mole_cations, as.numeric(telem['mole_wt',]));

    mole_oxigen <- rowApply('*', wtp_group, as.numeric(telem['noxygen',]));
    mole_oxigen <- rowApply('/', mole_oxigen, as.numeric(telem['mole_wt',]));

    norm_cations <- mole_cations;

    for(i in 1:nrow(norm_cations)) {
        if(norm_cations[i,]$Fe2O3_wtp>0) {
            norm_cations[i,] = norm_cations[i,] * 8/rowSums(mole_oxigen)[i];
        } else {
            norm_cations[i,] = norm_cations[i,] * 5/rowSums(mole_cations)[i];        
        }
    }
    
    norm_oxygens <- norm_cations;
    norm_oxygens <- rowApply('*', norm_oxygens, as.numeric(telem['noxygen',]));
    norm_oxygens <- rowApply('/', norm_oxygens, as.numeric(telem['ncations',]));

    names(norm_cations) <- pfu_names;
    charge <- 4*(norm_cations$Si_pfu+norm_cations$Ti_pfu)+
              3*(norm_cations$Al_pfu+norm_cations$Cr_pfu+norm_cations$Fe_p3_pfu)+
              2*(norm_cations$Fe_p2_pfu+norm_cations$Mn_pfu+norm_cations$Mg_pfu+norm_cations$Ca_pfu);
              
    pfu_units <- norm_cations;

    fecharge <- ifelse(16-charge>0,16-charge,0);
    pfu_units$Fe_p3_pfu <- ifelse(pfu_units$Fe_p3_pfu > 0, pfu_units$Fe_p3_pfu, fecharge);
    pfu_units$Fe_p2_pfu <- ifelse(norm_cations$Fe_p3_pfu > 0, pfu_units$Fe_p2_pfu, norm_cations$Fe_p2_pfu - pfu_units$Fe_p3_pfu);

    endcharge <- 4*(pfu_units$Si_pfu+pfu_units$Ti_pfu)+
                 3*(pfu_units$Al_pfu+pfu_units$Cr_pfu+pfu_units$Fe_p3_pfu)+
                 2*(pfu_units$Fe_p2_pfu+pfu_units$Mn_pfu+pfu_units$Mg_pfu+pfu_units$Ca_pfu);

    endcharge<- 16-endcharge;

    rownames <- data.frame(Name = wtp_data$Name);
    qcheck <- data.frame(ChargeDisbalance = endcharge);
 
    return (cbind(rownames, pfu_units, qcheck));
}

recalc.pl_nm.test <- function () {
    test <- data.frame(Name=c("Sp1","Sp2"), SiO2_wtp=c(38.03,38.03), Al2O3_wtp=c(12.91,12.91), FeO_wtp=c(5,0), Fe2O3_wtp=c(0,30.32), CaO_wtp=c(17.75, 17.75));

    result <- recalc.pl_nm(test);
    print(result);
    expect_equal(object = result[1,]$Fe_p2_pfu, 0.244, tolerance = 0.005);
    expect_equal(object = result[2,]$Al_pfu, 0.8, tolerance = 0.005);
}