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MW12_Minntac_InitCond_chem.m
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MW12_Minntac_InitCond_chem.m
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function [mob_eq_comp, mob_eq_ic_z, mob_eq_extra_z, min_eq_comp, min_eq_ic_z, ...
catex_comp, catex_ic_z, surf_comp, surf_ic_z, surf_par, surf_cpl, surf_calc_type] = ...
MW12_Minntac_InitCond_chem(phrq_sim_dir, phrq_exe, use_file_databas, por, tempC)
% Uses the following functions:
% - Alk2DIC() (only needed if data is for alkalinity)
% Converts alkalinity to total C(4)
% - generate_ic_PHREEQC_f_051915a()
% Generates equilibrated ic using PHREEQC
% - go_PHREEQC2_3()
% Called by generate_ic_PHREEQC_f_051915a(), runs PHREEQC
% % - ONLY uncomment below if running as script
% fl_gcng = 1; % 1 for gcng, 0 for Patrick
% if fl_gcng
% sim_dir = 'C:\Hydro_Modeling\pht3d_dir\';
% phrq_exe = 'C:\Hydro_Modeling\phreeqc.exe';
% use_file_databas = 'C:\Hydro_Modeling\pht3d_dir\pht3d_datab2.dat';
% else
% sim_dir = 'C:\Hydro_Modeling\pht3d_dir\';
% phrq_exe = 'C:\Hydro_Modeling\phreeqc.exe';
% use_file_databas = 'C:\Hydro_Modeling\pht3d_dir\pht3d_datab2.dat';
% end
% tempC = 10.0;
% por = 0.39;
% phrq_sim_dir = sim_dir;
% % **** To run as script: comment out 1st line for function, uncomment below
% % block
% SC_dir = '/home/gcng/workspace/matlab_files/SecondCreek';
% addpath(SC_dir);
% sim_dir = '/home/gcng/workspace/ModelRuns_scratch/PHT3D_projects/SecondCreek/test1_1D/';
% phrq_sim_dir = sim_dir;
%
% % you may not need this
% matlab_dir = '/home/gcng/workspace/matlab_files/my_toolbox/PHT3D_functions';
% addpath(matlab_dir);
% % ----------------
% *** CUSTOMIZE: **********************************************************
% This script uses PHREEQC to prepare (equilibrate and charge-balance)
% different aqueous solutions for use in initial and boundary conditions.
% Different aq solutions could correspond to different parts of the domain,
% e.g. Cell 2 water, bulk domain groundwater, and recharge water. These
% different aq solutions will be called 'zones'.
%
% Use this section to specify the number of zones and to comment on what
% each zone represents.
nzones = 3;
% ** comment here to describe 'zones'
% zone 1: cell 2 water
% zone 2: domain ic water
% zone 3: recharge water
% *************************************************************************
% -- SET MODEL CHEMISTRY: initial trial values
% (Units -- aq: mol/L_w, user-defined immob (e.g. bacteria, napl): mol/L_w,
% minerals (and gases): mol/L_v, exchangers and surfaces: mol/L_v)
% - mobile equil components
% (ic from PHREEQC batch run)
n_mob_eq_max = 50;
mob_eq_comp = cell(n_mob_eq_max,1);
mob_eq_obs_z = zeros(nzones, n_mob_eq_max);
convert_obs2model = zeros(1, n_mob_eq_max); % convert obs units to mol/L
mob_eq_extra_z = cell(nzones, n_mob_eq_max);
ii = 0;
ii=ii+1; mob_eq_comp{ii} = 'C(4)'; % ***********************************
Ka1 = 10^-6.3; Ka2 = 10^-10.3; KH = 10^-14;
pH = 6.92;
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; %Alk2DIC(3*5.19/1000, pH, Ka1, Ka2, KH); % meq/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; %Alk2DIC(3*5.19/1000, pH, Ka1, Ka2, KH); % meq/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; %Alk2DIC(3*5.19/1000, pH, Ka1, Ka2, KH); % meq/L
convert_obs2model(ii) = 1;
ii=ii+1; mob_eq_comp{ii} = 'Ca'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
convert_obs2model(ii) = 1/1000/40.08;
ii=ii+1; mob_eq_comp{ii} = 'Cl'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 141.557; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
convert_obs2model(ii) = 1/1000/35.453;
% mob_eq_extra_z{zz,ii} = 'charge';
ii=ii+1; mob_eq_comp{ii} = 'Fe(2)'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % ug Fe/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % ug Fe/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % ug Fe/L
convert_obs2model(ii) = 1/1e6/55.847;
ii=ii+1; mob_eq_comp{ii} = 'K'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
convert_obs2model(ii) = 1/1e3/39.102;
ii=ii+1; mob_eq_comp{ii} = 'Mg'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
convert_obs2model(ii) = 1/1e3/24.312;
ii=ii+1; mob_eq_comp{ii} = 'Mn(2)'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % ug/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % ug/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % ug/L
convert_obs2model(ii) = 1/1e6/54.938;
ii=ii+1; mob_eq_comp{ii} = 'Na'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 6.89; % mg/L 'charge' denotes will balance with anions
mob_eq_extra_z{zz,ii} = 'charge';
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
mob_eq_extra_z{zz,ii} = 'charge';
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
mob_eq_extra_z{zz,ii} = 'charge';
convert_obs2model(ii) = 1/1e3/22.9898;
ii=ii+1; mob_eq_comp{ii} = 'O(0)'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 100; % mg/L DO
zz = zz + 1; mob_eq_obs_z(zz,ii) = 10; % mg/L DO
zz = zz + 1; mob_eq_obs_z(zz,ii) = 10; % mg/L DO
convert_obs2model(ii) = 1/1e3/16.0;
ii=ii+1; mob_eq_comp{ii} = 'S(-2)'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg S/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg S/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg S/L
convert_obs2model(ii) = 1/1e3/32.064;
ii=ii+1; mob_eq_comp{ii} = 'S(6)'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 918.172; % mg SO4/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg SO4/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg SO4/L
convert_obs2model(ii) = 1/1e3/(32.064+4*16.0);
ii=ii+1; mob_eq_comp{ii} = 'Si'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
convert_obs2model(ii) = 1/1e3/28.0843;
ii=ii+1; mob_eq_comp{ii} = 'C(-4)'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
zz = zz + 1; mob_eq_obs_z(zz,ii) = 0; % mg/L
convert_obs2model(ii) = 1/1e3/16.0;
ii=ii+1; mob_eq_comp{ii} = 'pH'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 6.92; %
zz = zz + 1; mob_eq_obs_z(zz,ii) = 6.92; %
zz = zz + 1; mob_eq_obs_z(zz,ii) = 6.92; %
convert_obs2model(ii) = 1;
ii=ii+1; mob_eq_comp{ii} = 'pe'; % ***********************************
zz = 0;
zz = zz + 1; mob_eq_obs_z(zz,ii) = 14; %
zz = zz + 1; mob_eq_obs_z(zz,ii) = 14; %
zz = zz + 1; mob_eq_obs_z(zz,ii) = 14; %
convert_obs2model(ii) = 1;
n_mob_eq = ii;
mob_eq_comp = mob_eq_comp(1:n_mob_eq);
mob_eq_obs_z = mob_eq_obs_z(:,1:n_mob_eq);
mob_eq_extra_z = mob_eq_extra_z(:,1:n_mob_eq);
convert_obs2model = convert_obs2model(1:n_mob_eq);
mob_eq_obs_z = mob_eq_obs_z .* repmat(convert_obs2model, nzones, 1);
% - mineral eq components
% (only allowed for porewater solution)
n_min_eq_max = 10;
min_eq_comp = cell(n_min_eq_max,1);
min_eq_ic_z = zeros(nzones,n_min_eq_max);
ii = 0;
% ii=ii+1; min_eq_comp{ii} = 'Fe(OH)3(a)'; % ***********************************
% min_eq_ic_z(zz,ii) = 10; % arbitrary conc
% ii=ii+1; min_eq_comp{ii} = 'Gibbsite'; % ***********************************
% min_eq_ic_z(zz,ii) = 30e-6*rho_b; % (mol/Lv)
% ii=ii+1; min_eq_comp{ii} = 'Goethite'; % ***********************************
% min_eq_ic_z(zz,ii) = 50e-6*rho_b; % (mol/Lv)
% ii=ii+1; min_eq_comp{ii} = 'Pyrolusite'; % ***********************************
% min_eq_ic_z(zz,ii) = .25e-6*rho_b; %
% ii=ii+1; min_eq_comp{ii} = 'Siderite'; % ***********************************
% min_eq_ic_z(zz,ii) = 10; % arbitrary conc
ii=ii+1; min_eq_comp{ii} = 'FeS(ppt)'; % ***********************************
zz = 0;
zz = zz + 1; min_eq_ic_z(zz,ii) = 0; % 0 mineral in Cell 2 water
zz = zz + 1; min_eq_ic_z(zz,ii) = 0; % arbitrary conc
zz = zz + 1; min_eq_ic_z(zz,ii) = 0; % arbitrary conc
% zz = zz + 1; min_eq_ic_z(zz,ii) = 10; % arbitrary conc
% zz = zz + 1; min_eq_ic_z(zz,ii) = 10; % arbitrary conc
% ii=ii+1; min_eq_comp{ii} = 'Rhodochrosite'; % ***********************************
% ii=ii+1; min_eq_comp{ii} = 'Vivianite'; % ***********************************
n_min_eq = ii;
min_eq_comp = min_eq_comp(1:n_min_eq);
min_eq_ic_z = min_eq_ic_z(:,1:n_min_eq);
% - catex components (catex_exch is exchanger site)
n_catex_exch_max = 10;
catex_exch_comp = cell(n_catex_exch_max,1);
catex_exch_ic_z = zeros(nzones, n_catex_exch_max);
ii = 0;
n_catex_exch = ii;
catex_exch_comp = catex_exch_comp(1:n_catex_exch);
catex_exch_ic_z = catex_exch_ic_z(:,1:n_catex_exch);
% - catex components (catex is exchanger sorbed compound)
% (ic from PHREEQC batch run)
n_catex_max = 10;
catex_comp = cell(n_catex_max,1);
ii = 0;
n_catex = ii;
catex_comp = catex_comp(1:n_catex);
% - surface complexation components
% **** WARNING: not set up for surfaces w/
% multiple sites (would need to enter only 1 surf_calc_type
% per surface in _ph file)
n_surf_max = 10;
surf_comp = cell(n_surf_max,1);
% surf_ic: number of sites [mol/Lv] if not coupled to phase or reactant,
% (number of sites per mol x porosity) [mol/mol] if coupled
surf_ic_z = zeros(nzones,n_surf_max);
% surf_par(1,ii): SurfArea ([m2/g] if not coupled to phase or reactant,
% [mol/m2] if coupled to phase or reactant)
% surf_par(2,ii): mass ([g/L] if not coupled to phase or reactant,
% include but ignored if coupled to phase or reactant)
surf_par = zeros(2,n_surf_max);
% surf_cpl{1,ii}: Empty if not coupled to phase or reactant
% surf_cpl{1,ii}: Name of pure phase or kin reactant coupled to
% surf_cpl{2,ii}: 'equilibrium_phase' to couple to pure phase, or
% 'kinetic_reactant' to couple to kinetic reactant
surf_cpl = cell(2,n_surf_max);
surf_calc_type = '';
ii = 0;
n_surf = ii;
surf_comp = surf_comp(1:n_surf);
surf_ic_z = surf_ic_z(:,1:n_surf);
surf_par = surf_par(:,1:n_surf);
% (done setting model chemical components)
% - select output list
phrq_sel_outlist.total = [mob_eq_comp(~strncmp('p',mob_eq_comp,1))];
phrq_sel_outlist.mol = catex_comp;
phrq_sel_outlist.equilphase = min_eq_comp;
phrq_sel_outlist.si = []; phrq_sel_outlist.gas = [];
% -- Get initial conditions w/ PHREEQC
% % (re-)run PHREEQC to equilibrate ic conc for each zone
% fprintf('Have not finished code of fl_init_phrq=1! Need to do for each zone! Exiting...\n');
% return
mob_eq.name = mob_eq_comp; mob_eq.extra_z = mob_eq_extra_z;
if n_catex == 0 % not cation exchange components
catex = [];
else
% assume exchanger is same for all zones
catex.name = catex_exch_comp;
catex.cec = catex_exch_ic / por;
end
fl_force_redox = 1; % force redox equilibration, not just charge balance
% -- Set file names
phrq_infil = fullfile(phrq_sim_dir, 'batch_phrq.dat');
phrq_outfil = fullfile(phrq_sim_dir, 'batch_phrq.out');
phrq_tblfil = fullfile(phrq_sim_dir, 'batch_phrq.tbl');
phrq_sel_outfil = fullfile(phrq_sim_dir, 'batch_phrq.sel');
% set database file (must be in sim_dir with file name 'pht3d_datab.dat')
file_databas = fullfile(phrq_sim_dir, 'pht3d_datab.dat');
copyfile(use_file_databas, file_databas);
% -- Check to make sure you don't over-write any output files
% - go to simulation dir (check to make sure not over-writing, no current programs running)
if ~exist(phrq_sim_dir, 'dir')
mkdir(phrq_sim_dir);
end
%if exist([phrq_sel_outfil, '1'], 'file')
% fprintf('phrq_sim_dir has .sel file(s)! Could be job running or unsaved job there. Exiting...\n');
% fprintf('(phrq_sim_dir %s) \n', phrq_sim_dir);
% mob_eq_comp = []; mob_eq_ic_z = []; mob_eq_extra_z = []; min_eq_comp = []; min_eq_ic_z= [];
% catex_comp = [];catex_ic_z = [];surf_comp = [];surf_ic_z = [];surf_par = [];surf_cpl = [];surf_calc_type = [];
% return
%end
% -- Run PHREEQC to equilibrate and charge-balance aq solutions for each zone
units = 'mol/kgw';
mob_eq_ic_z = zeros(nzones, n_mob_eq);
catex_ic_z = nan(nzones, n_catex);
for zz = 1:nzones % loop through different zones
fprintf('\n--- Zone %d ---', zz);
mob_eq.ic = mob_eq_obs_z(zz,:);
mob_eq.extra = mob_eq_extra_z(zz,:);
phase.name = min_eq_comp; phase.ic = min_eq_ic_z(zz,:);
phase.si = zeros(n_min_eq,1);
[mob_eq_ic_z(zz,:), b] = generate_ic_PHREEQC_f_062215a_2(...
phrq_exe, phrq_infil, phrq_outfil, file_databas, phrq_sel_outfil, phrq_sel_outlist, ...
por, tempC, units, ...
mob_eq, phase, catex, ...
mob_eq_comp, catex_comp, fl_force_redox, ...
phrq_tblfil);
if ~isempty(b)
catex_ic_z(zz,:) = b;
end
movefile(phrq_infil, [phrq_infil, num2str(zz)]);
movefile(phrq_outfil, [phrq_outfil, num2str(zz)]);
movefile(phrq_sel_outfil, [phrq_sel_outfil, num2str(zz)]);
movefile(phrq_tblfil, [phrq_tblfil, num2str(zz)]);
end