Version 3.1.6: January 20, 2015 Version 3.1.5: December 18, 2014 -------- svn 9084 -------- Fixed warnings identified by CRAN. -------- svn 9073 -------- Aqueous species H+ was missing from the list of species returned by SYS("aq", count, name$, type$, moles). -------- svn 9072 -------- Added Basic function diff_c, which returns the diffusion coefficient for a species at 25 C. For example, d = DIFF_C("CO3-2") -------- svn 9029 -------- In inverse modeling, the writing of input files for NetpathXL was incorrect. Revisions to the program had eliminated a speciation calculation necessary to provide the correct values. -------- svn 9000 -------- Kinetic names were not saved correctly to allow unique retrival by name. The error could have lead to misidentification of kinetic reactions for a cell. -------- svn 8957 -------- Uninitialized variable for commands of USER_PUNCH. Version 3.1.4: August 20, 2014 -------- svn 8925 -------- Molar volume was not calculated correctly in mixing a gas. -------- svn 8923 -------- Acentric factor for H2(g) had positive sign. Corrected to negative for H2(g) and Hdg(g) in phreeqc.dat, Amm.dat, and pitzer.dat. -------- svn 8919 -------- When a batch kinetic reaction was simulated, followed by a transport simulation with kinetics, the time was not reset between the two simulations. Version 3.1.3: August 6, 2014 -------- svn 8895 -------- Missing initializations in class_main. -------- svn 8879 -------- Pressure was incorrect in mix of GAS_PHASE. Also fixed a NULL pointer when the element in a gas phase was missing from the system. -------- svn 8875 -------- Error reading dump of SURFACE when using no_edl option. -------- svn 8847 -------- Series of changes to correct memory leaks, uninitialized variables, variables set but not used, and other warnings detected by Valgrind and Visual Studio. -------- svn 8756 -------- Relative dielectric constant was not calculated correctly. -------- svn 8755 -------- Basic function LK_SPECIES was changed to use the the log K as found in the SOLUTION_SPECIES definition. Previously, the log K was for the equations rewritten to the current master species. -------- svn 8741 -------- Handling of isotopes uncertainty was inconsistent with documentation in INVERSE_MODELING. Also missing defaults for O and H redox states. -------- svn 8628 -------- Entities with negative user numbers are not dumped. -------- svn 8622 -------- Modifications to meet R requirements. -------- svn 8576 -------- Fixed error when Pitzer or SIT parameter was redefined. Version 3.1.2: March 1, 2014 -------- svn 8532 -------- Changed the way the pressure is assigned to a fixed-pressure gas phase in a reaction calculation. Previously, pressure of the gas phase did not change (unless GAS_PHASE_MODIFY was used). Now, if REACTION_PRESSURE is defined, it is used for the fixed pressure of the gas. -------- svn 8520 -------- Changes in MCD to accomodate unequal cell lengths. -------- svn 8502 -------- Modified not to DUMP temporary entities with negative user numbers. -------- svn 8484 -------- Modified to allow diffusion calculations in TRANSPORT with unequal cell lengths. -------- svn 8469 -------- Logic for connecting points in USER_GRAPH was revised. -------- svn 8453 -------- Error where punch file was deleted twice if there was a Basic error. No longer an error if you try to modify a non-existing entity (SOLUTION, EXCHANGE, etc), only a warning. -------- svn 8378 -------- Removed yellow from colors for graphing; it was sometimes hard to see. Changed Li molar volume in pitzer.dat, Amm.dat, and phreeqc.dat. ------------- svn 8371-8375 ------------- Multiple bug fixes pointed out by Marco De-Vroed. Set basic_interpreter to NULL after deleting. Revised handling of initial data for initial-solution calculations. Revised logic for switching to numerical derivatives for high-pressure calculations, the variable switch_numerical was removed. -------- svn 8356 -------- Fixed bug with solution volume in initial solutions containing Alkalinity. -------- svn 8301 -------- Density was not stored with the solution after a calculation. -------- svn 8293 -------- Solution volume was not initialized in zero(), and pressure was not set correctly when mixing solutions. Version 3.1.1: December 6, 2013 -------- svn 8203 -------- Updated more molar volumes in phreeqc.dat, Amm.dat, and pitzer.dat. Mn+2, Al+3, PO4-3, F-, Li+, Br-, Zn+2, Cd+2, Cu+2, NH4+, HPO4-2, H2PO4-, and H3PO4, and other related ion pairs or complexes. Also estimated more ion size parameters for pairs and complexes. Molar volume approach is published in Appelo, Parkhurst, and Post, 2013, Geochimica et Cosmochimica Acta, v. 125, p. 49-67. -------- svn 7997 -------- Modified chart handling for PhreeqcI to allow charts from multiple runs to remain open for comparison. Charts will remain visible until closed. -------- svn 7992 -------- Identifier -high_precision was added to the PRINT data block to allow higher precision for the PRINT Basic command, which is generally used in USER_PRINT definitions. -------- svn 7987 -------- Now can have multiple SELECTED_OUTPUT n and USER_PUNCH n. SELECTED_OUTPUT 1 has the same functionality as previous versions of SELECTED_OUTPUT, with a set of default print definitions. SELECTED_OUTPUT n, where n is not equal to 1, has no fields initially defined; it is equivalent to an automatic -reset false. A file may be defined for each SELECTED_OUTPUT n that will recieve the output from the data block. Using i to represent a specific integer, USER_PUNCH i will write to the file defined for SELECTED_OUTPUT i. If USER_PUNCH i is defined, but SELECTED_OUTPUT i is not, then no data will be written from USER_PUNCH i. Printing to the selected-output files is controlled by three identifiers. PRINT; -selected_output true/false will enable/disable printing of all selected-output files. For an individual SELECTED_OUTPUT i definition, -active true/false will enable/disable both SELECTED_OUTPUT i and USER_PUNCH i. Again for SELECTED_OUTPUT i, -user_punch true/false will enable/ disable the USER_PUNCH i data (rarely used). If SELECTED_OUTPUT i has been defined, a new data block of SELECTED_OUTPUT i will retain the previous definition if only -active and (or) -user_punch are defined. Defining any other identifier will cause the old definiton to be removed and its file closed; the data for SELECTED_OUTPUT i will be defined entirely by the new data block. -------- svn 7962 -------- Database modifications: pitzer.dat: Parameters have been reordered to alphabetical order. phreeqc.dat and Amm.dat: Vm refit for aqueous species Na+, CO3-2, SO4-2, NO3-, HCO3-, NaCO3-, NaHCO3, NaSO4, KSO4. Analytical expression adjusted for gypsum, anhydrite, and sylvite (delta H). -------- svn 7916 -------- Addition of a temperature-dependent pressure correction for the Debye-Hueckel term for the Pitzer formulation. An empirical, temperature-dependent pressure correction has been introduced in the Debye-Hueckel part of Pitzer's equation for gamma (activity coefficient), which lets the factor B vary from 1.2 to 1. Pitzer defined this number to be 1.2 for all pressures and temperatures. For monovalent species the correction is: pap = (7e-5 + 1.93e-9 * (TK - 250)^ 2.0) * patm_x For divalent species the correction is: pap = (9.65e-10 * (TK - 263)^ 2.773) * (patm_x^0.623) In both cases, pap is limited to less than 0.2. The factor B in the Debye-Hueckel factor is B = 1.2 - pap The Debye-Hueckel factor is F = = -A0 * (DI / (1.0 + B * DI) + 2.0 * log(1.0 + B * DI) / B) where DI is the square root of the ionic strength. -------- svn 7972 -------- A revised version of the manual is now distributed as a compiled HTML file (phreeqc3.chm). It has corrections and new features highlighted in forest green. -------- svn 7920 -------- GAS_PHASE processing was incorrect for fixe-volume gas with multiple components. The wrong number of moles of gas some gas components was calculated. -------- svn 7896 -------- The manual wording was wrong or confusing in some places regarding the difference between fugacity (F) and (partial) pressure (P) of a gas. For ideal gases, P = F. However for Peng-Robinson gases F = P * phi / 1 atm (unitless). In EQUILIBRIUM_PHASES, the target saturation index for a gas is log10(P). In SELECTED_OUTPUT -saturation_index, for gases, the value printed will be the fugacity. For Basic functions SI and SR, the values are based on the fugacity. P and phi can be obtained with the Basic functions PR_P and PR_PHI. For the Saturation Index block of the output file, the SI for a gas is its fugacity. However, for Peng-Robinson gases, P and phi are appended to the output line. -------- svn 7884 -------- IPHREEQC: added a Basic function, CALLBACK, which allows data be passed to and from the calling program. The new IPhreeqc method is for C, iresult = SetBasicCallback(ID, function name, cookie) and for Fortran, iresult = SetBasicFortranCallback(ID, function name) The two methods are necessary because arguments are handled differenctly between C and Fortran. The void pointer cookie in the C callback can be used to allow the user-defined callback function to find necessary data. The user-defined function for C must be of the form double my_callback(double, double, const char *, void *) For Fortran the function must be of the form double precision my_callback(double precision, double precision, character(*)) As an example, to get the current time for a calculation, the callback could be used as follows: Basic: 10 date = CALLBACK(dummy, dummy, "Year") Fortran after registering my_callback by using SetBasicFortranCallback double precision function my_callback(x1, x2, string) USE date_module, only: year double precision x1, x2, my_callback character(*) string if (string .eq. "Year") then return dble(year) endif end A usage of the callback feature has been added to the IPhreeqc example advect for Fortran, C, and C++. Additional documentation is in the .chm documentation files for IPhreeqc. -------- svn 7867 -------- SOLUTION_MODIFY and SOLUTION_RAW were missing the -pressure identifier. It has now been added. -------- svn 7857 -------- Trapped error when solid-solution components were not defined correctly. -------- svn 7855 -------- Error in pressure dependence when Pitzer or SIT aqueous model was used. The pressure dependence was not calculated if the pressure was changed, but the temperature was not. -------- svn 7829 -------- Added Basic fuction EQUIV_FRAC that returns the equivalent fraction of a surface or exchange species. The three arguments are (1) Species name (input), (2) Equivalents of exchange or surface sites per mole of the species (output), (3) The name of the surface or exchange site (output). For example, 10 f = EQUIV_FRAC("AlX3", eq, x$) f = equivlalent fraction of AlX3 relative to total equivalents of X sites. eq = 3.0 x$ = "X" If the species name is not found to be a surface or exchange species, the return value is 0, the second argument is set to 0, and the third argument is set to an empty string. Also added synonyms for Basic functions PHASE_FORMULA and SPECIES_FORMULA with trailing $ signs--PHASE_FORMULA$ and SPECIES_FORMULA$. To be consistent with Basic, the functions should have $ signs because they return strings. -------- svn 7828 -------- Added Basic fuction SPECIES_FORMULA that returns the stoichiometry of an aqueous, exchange, or surface species. The function returns a string: "aq" for aqueous, "ex" for exchange, "surf" for surface, and "none" if there is no species of that name. The four arguments are (1) the name of the species (input), (2) the number of elements, including charge (output), (3) an string array of element names (output), (4) a number array of coefficients corresponding to the elements (output). The following example: 10 name$ = "AlX3" 20 ty$ = SPECIES_FORMULA(name$, count_s, elt$, coef) 20 print pad(name$, 15), ty$ 30 for j = 1 to count_s 40 print pad(blank$, 5), pad(elt$(j),5), str_f$(coef(j), 5, 0) 50 next j Produces the following output: AlX3 ex Al 1 X 3 charge 0 -------- svn 7781 -------- Basic function SYS("phases",...) returned 0.0, rather than the maximum saturation index if the maximum saturation index was less than zero. Now returns the maximum saturation index even if it is less than zero. Added new Basic function STR_E$(x, w, d) that produces a string with exponential format from a number with a given width (w) and number of decimal places (d). w is the minimum width of the string. The string is padded with spaces to the left to produce a string of the specified width (w); however, the string will be wider than w characters, if the number does not fit in the specified width. If x = 123456.789, then STR_E$(x,15,5) produces the following on a Windows computer: 1.23457e+005 -------- svn 7766 -------- Added new Basic function STR_F$(x, w, d) that produces a string from a number with a given width (w) and number of decimal places (d). w is the minimum width of the string. The string is padded with spaces to the left to produce a string of the specified width (w); however, the string will be wider than w characters, if the number does not fit in the specified width. If x = 123456.789, then STR_F$(x,15,5) produces the following on a Windows computer: 123456.78900 -------- svn 7763 -------- Fixed bug with isotopes. Moles and molalities were incorrect if the mass of water in the SOLUTION was not 1.0. Version 3.0.6: June 4, 2013 -------- svn 7757 -------- Fixed bug introduced in version 3.0.5 if two DELETE keywords were used in a run. Fixed a bug with fixed- pressure gas, where the volume was 1.0 even when no moles of gas were present in the gas phase. Minor optimizations for initialization of Peng-Robinson gas data. Version 3.0.5: May 31, 2013 -------- svn 7748 -------- Optimizations for equilibrium phases, using pointers instead of lookup function. Other optimizations for SURFACE calculations to limit uses of std::map find, eliminate strcmps, and skip inverse setup when not needed. Minor fix to Peng Robinson. Fixed bug with SOLUTION_MODIFY when a concentration was set to zero. Removed lower limit on ionic strength. Version 3.0.4: May 14, 2013 -------- svn 7703 -------- Fixed bug in PhreeqcI that caused no warnings to be included in the output file. -------- svn 7677 -------- Gas-phase volume was not correct in SELECTED_OUTPUT -gas printout for Peng-Robinson calculations. -------- svn 7677 -------- Added KIN_TIME Basic function, which gives the time interval in seconds of the last kinetic integration. KIN_DELTA("xxx")/KIN_TIME will give the average rate over the time interval for reaction xxx. For example, KINETICS Calcite -m 1 -step 864 8640 KIN_TIME will return 864 after the first step and 8640 after the second. The result of KIN_TIME will be the same whether INCREMENTAL_ REACTIONS is true or false (although TOTAL_ TIME will differ). Version 3.0.3: April 30, 2013 Fixed errors in GAS_PHASE, -fixed_pressure used the sum of the input pressures instead of the defined total pressure in some cases, set upper limits in PR calculations; revised Basic function LK_SPECIES; logic for printing status line revised; fixed bug in SOLUTION_SPREAD, mass of water was not read properly; fixed problem with spaces in output file name; revised logic for checking if opening files was successful, old C-style check was incorrect; revised molar volume definitions and selected parameters in databases phreeqc.dat, Amm.dat, and pitzer.dat Version 3.0.2: April 4, 2013 Fixed an initialization error for activity of water that caused slow convergence. Dump wrote a file that caused read errors when some names exceeded 21 characters. Gas_phase_modify did not work correctly. Version 3.0.1: March 21, 2013 Fixed bug in printing of solid solutions that caused a crash. The pressure dependence of log K in the printout of the equilibrium phases assemblage in the saturation index list was incorrect. Version 3.0.0: February 1, 2013 PHREEQC Version 3 is finally released. Major new features include pressure dependence for geochemical reactions, the nonideal gas formulation of Peng and Robinson, and charting. All features of PHREEQC Version 3 are documented in U.S. Geological Survey Techniques and Methods 6-A43, “Description of input and examples for PHREEQC Version 3--A computer program for speciation, batch-reaction, one- dimensional transport, and inverse geochemical calculations”, available at https://pubs.usgs.gov/tm/06/a43/. Features not previously documented include Pitzer and SIT aqueous models, CD-MUSIC surface complexation, isotopic capabilities, and new keyword data blocks to manipulate reactants, such as RUN_CELLS, DELETE, COPY, _MODIFY, _RAW, and DUMP. ************************************************************ ************************************************************ * All features of PHREEQC Version 3 are * * documented in Techniques and Methods 6-A43. * ************************************************************ ************************************************************ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ************************************************************ * Features in PHREEQC++ Not in PHREEQC version 2 * * PHREEQC++ is used only in IPhreeqc Modules * * Revisions and Bug Fixes * ************************************************************ ------------------------------------------------------------ Version 2.18.2: April 9, 2011 ------------------------------------------------------------ -------- svn 5471 -------- Added PHASE_FORMULA and LIST_S_S Basic functions. PHASE_FORMULA returns a string value with the chemical formula for the phase as defined in PHASES data. If 4 arguments are provide, a list of the elements and stoichiometric coefficients for elements are returned. USER_PRINT 10 min$ = "Calcite" 20 form$ = PHASE_FORMULA(min$) 30 print min$, form$ 40 form$ = PHASE_FORMULA(min$, count, elts$, coefs) 50 for i = 1 to count 60 print " ", PAD(elts$[i], 20), coefs[i] 70 next i This example produces the following output: Calcite CaCO3 C 1 Ca 1 O 3 LIST_S_S returns the sum of moles of all components in a specified solid solution. Lists of the components and the number of moles of each component are also returned. SOLID_SOLUTIONS 1 Calcite_s_s -comp Calcite 0.01 -comp Smithsonite 0.001 -comp Strontianite 0.02 USER_PRINT 10 name$ = "Calcite_s_s" 20 total = LIST_S_S(name$, count, comp$, moles) 30 print PAD(name$, 20), total 40 for i = 1 to count 50 print " ", PAD(comp$[i], 20), moles[i], moles[i]/total 60 next i This example produces the following output: Calcite_s_s 3.0876e-002 Calcite 9.9316e-003 3.2166e-001 Smithsonite 9.6666e-004 3.1308e-002 Strontianite 1.9978e-002 6.4704e-001 -------- svn 5455 -------- REACTION_MODIFY keyword was added to the modules. Previously, REACTION_MODIFY was not recognized as a keyword. -------- svn 5453 -------- Fixed bug with in READ_SOLUTION_RAW. A read error occurred when -isotopes was encountered. -------- svn 5448 -------- Reading of default user number, but specified description was in error under some conditions. -------- svn 5431 -------- RUN_CELLS was rewritten to perform multiple calculations if multiple steps are defined in REACTION, REACTION_TEMPERATURE, or KINETICS. It now operates in the same way that a series of USE and SAVES would operate. Previously, only one step of a series of reaction steps was taken. If a time step is provided in RUN_CELLS for kinetic reactions and nmax is the maximum number of steps defined for REACTION, REACTION_TEMPERATURE, and KINETICS, the time step is divided into nmax equal increments. It is equivalent to the following definition in kinetics: -step time_step in nmax steps. -------- svn 5324 -------- Modified solution method for solid solutions so that mole transfers were limited to the total amount available in the system. ------------------------------------------------------------ Version 2.18.0: April 9, 2011 ------------------------------------------------------------ -------- svn 5281 -------- If SOLUTION_MODIFY is used to change a total for an element, the activities for the master species of the element are automatically updated by the ratio of the new total to the old total, unless activities are specifically set for the element with -activities. All valence states of redox elements are adjusted. -------- svn 5270 -------- Added logic to update estimates of log activity when modifying totals in SOLUTION_MODIFY. The initial guesses for activities are adjusted proportionally to the change in total moles of elements (as defined by SOLUTION_MODIFY; -totals). This automatic adjustment is suggested rather than explicit definition of the initial guesses through SOLUTION_MODIFY; -activities. However, the -activities identifier may be used and will supercede the automatic adjustment. The adjustment of the initial guesses for activities should reduce the number of iterations needed to solve a given set of equations and, consequently, should lessen the total CPU time for a simulation. -------- svn 4897 -------- Added capability to include files within the input file. Files included in include files are also included. Files are included verbatim and need not contain complete keyword datablocks; however, the combination of included files must result in a legal PHREEQC input file. Files are included as simulations are proceeding, so it is possible to write a file at one point of a run that is included later in the same run. Included files can contain INCLUDE$ directives. SOLUTION INCLUDE$ file_name END where "file_name" contains: EQUILIBRIUM_PHASES Calcite 0 10 is the same as a single file with SOLUTION EQUILIBRIUM_PHASES Calcite 0 10 END -------- svn 4856 -------- Revised logic of searching pitzer parameters so that order of ions in a parameter definition does not matter. -------- svn 4823 -------- Added -cells to DUMP and DELETE; cell option to COPY. Example: COPY cell 1 4 COPY cell 1 5-10 DUMP -cell 1 2-3 10 DELETE -cell 1-3 4 8-10 COPY cell n range The cell option of the COPY keyword causes all reactants defined with identifying number n to be copied to a single range of numbers. The range of numbers can be a single number or a range of numbers given by an integer, a hyphen, and an integer, with no intervening spaces. DUMP -cell list The -cell option writes _RAW formatted output to a specified file(see below for more details) for each reactant that is defined in the list. DUMP -cell list The -cell deletes from memory all reactants that are defined with identifying numbers in the list. The list of numbers for DUMP and DELETE are more flexible than for COPY. A list of ranges can be given for DUMP and DELETE, where each element of the list can be a single number or a range of numbers defined by an integer, a hyphen, and an ingeger, with no intervening spaces. -------- svn 4816 -------- Added compile capability to use #include file_name in input and database files. PHREEQCPP process the files at the start of the run, possibly following multiple layers of include files, to produce a stream that is then used as input. Compile define is MERGE_INCLUDE_FILES; PHREEQC_CLASS also must be defined. Input file: SOLUTION 1 #INCLUDE t2 #include t4 END File t2: REACTION NaCl 1 mmol #include t3 File t3: REACTION_TEMPERATURE 10 20 30 File t4: SAVE solution 1 When compiled with the include file #defines, the above set of files produces the following input for PHREEQC: SOLUTION 1 REACTION NaCl 1 mmol REACTION_TEMPERATURE 10 20 30 SAVE solution 1 END -------- svn 4800 -------- Added capability to dump REACTIONs, REACTION_TEMPERATUREs, and MIXes. DUMP -mix 1 4 6 -reaction 1-5 -reaction_temperature 1 3-9 List of numbers may be formatted as described for DUMP. Data are written in a format suitable for an input file to PHREEQCPP. Example of dumped keywords: MIX 1 1 0.33 2 0.33 3 0.34 REACTION_RAW 1 -units Mol -reactant_list Ba 1 Br 2 -element_list -steps 0.01 -equal_increments 1 -count_steps 2 REACTION_TEMPERATURE_RAW 1 -count_temps 3 -equal_increments 1 -temps 25 45 -------- Added -cells option to DUMP. DUMP -cells 1-19 20 This -cells option will dump any reactant with numbers between 1 and 20, including SOLUTIONs, EXCHANGERs, GAS_PHASEs, KINETICS, SOLID_SOLUTIONs, SURFACEs, REACTIONs, REACTION_TEMPERATUREs, and MIXes. -------- svn 3730 -------- Added keyword RUN_CELLS. RUN_CELLS -cells 1 2 5-6 7 -time_step 10000 -start_time 100 For each i listed in -cells it is the equivalent of the following: USE solution i USE equilibrium_phases i USE exchange i USE surface i USE solid_solution i USE gas_phase i USE kinetics i USE reaction i USE reaction_temperature i SAVE solution i SAVE equilibrium_phases i SAVE exchange i SAVE surface i SAVE solid_solution i SAVE gas_phase i If MIX i is defined, it is used in place of USE solution i. A MIX i or SOLUTION i must be defined to use RUN_CELLS; -cells i. All other entities are used only if they are defined. -start_time and -time_step are needed if any kinetic reactions are calculated. -start_time is the time at the start of the calculation, and -time_step is the length of time over which to integrate the kinetic reactions. -------- svn 3727 -------- Added keywords to allow modification of each reactant. A reactant must have been defined previously, but then each data item of the reactant can be changed and new components added. Data items read are changed, all other data items remain the same. Input format is the same as the RAW formats produced by DUMP. New keywords are as follows: SOLUTION_MODIFY EQUILIBRIUM_PHASES_MODIFY EXCHANGE_MODIFY SURFACE_MODIFY SOLID_SOLUTIONS_MODIFY GAS_PHASE_MODIFY KINETICS_MODIFY The example below is indented to indicate which information is necessary to change a data item. Working back through the indention levels for and item, each heading of a lower order is necessary to define the data item. In the example below, to change the number of moles of barite from 10 to 5 in the equilibrium phase assemblage, it is necessary to define EQUILIBRIUM_PHASES_MODIFY 1; -component; -name Barite; -moles 5. Items identified by an asterisk are most likely to consider for redefinition. Items with (*) are marked to indicate that care is needed to maintain charge balance relations. Unwanted redox and pH reactions may result from incorrect redefinition of these quantities. Items not marked are either initial estimates of variables calculated in the simulation, or are parameters thought not likely to be changed. The MODIFY data blocks change the data in the PHREEQC storage structures. They do not cause any initial composition calculations. Neither do they generate default reactions to be simulated. USE statements are needed to specify explicitly the desired reactions. SOLUTION_MODIFY 1 -temp 25 * -total_h 111.01243359981 (*) -total_o 55.506216800086 (*) -cb -3.6579285790756e-010 (*) -totals Cl 0.0010000000000003 (*) H(0) 1.4155655514601e-025 (*) Na 0.0010000000000003 (*) -Isotopes -pH 7 -pe 4 -mu 0.0010001035690258 -ah2o 0.99996599647757 -mass_water 1 -total_alkalinity 3.6579283856577e-010 -activities Cl -3.0155266404974 E -4 H(0) -25.15 Na -3.0153891985103 O(0) -42.080029535586 -gammas EQUILIBRIUM_PHASES_MODIFY 1 -eltList Ba 1 O 4 S 1 -component * -name Barite -si 0 * -moles 10 * -delta 0 -initial_moles 0 -force_equality 0 -dissolve_only 0 -precipitate_only 0 EXCHANGE_MODIFY 1 -pitzer_exchange_gammas 1 -component -formula X -totals Na 1.0000000058717 (*) X 1.0000000058717 (*) -charge_balance 0 -moles 0 -la 3.0000000302372 -phase_proportion 0 -formula_z 0 -formula_totals X 1 SURFACE_MODIFY 1 . -type 2 -dl_type 0 -sites_units 0 -only_counter_ions 0 -thickness 1e-008 -debye_lengths 0 -DDL_viscosity 1 -DDL_limit 0.8 -transport 0 -component -formula Hfo_s -formula_z 0 -moles 0 -la -0.11486188676541 -charge_balance 3.7853465372651e-005 -phase_proportion 0 -Dw 0 -formula_totals Hfo_s 0.01 -totals H 0.01003785346547 (*) Hfo_s 0.010000000000097 (*) O 0.010000000000097 (*) -charge_component -name Hfo -specific_area 600 -grams 1 -charge_balance 3.7853465372651e-005 (*) -mass_water 0 -la_psi 0.55146269389617 -la_psi1 0 -la_psi2 0 -capacitance0 1 -capacitance1 5 -diffuse_layer_totals SOLID_SOLUTIONS_MODIFY 1 -solid_solution -name Calcite -a0 0 -a1 0 -ag0 0 -ag1 0 -miscibility 0 -xb1 0.0 -xb2 0.0 -component calcite 0.1 * siderite 0.001 * GAS_PHASE_MODIFY 1 -type 0 -total_p 1 -volume 1 -component CO2(g) 1.4305508698401e-005 * KINETICS_MODIFY 1 -step_divide 1 -rk 1 -bad_step_max 500 -use_cvode 0 -cvode_steps 100 -cvode_order 5 -component -rate_name Calcite -tol 1e-008 -m 0.9999999999991 * -m0 1 -moles 8.9805940461929e-013 -namecoef CaCO3 1 -d_params 1 1 1 1 * -totals C 8.9801193858101e-013 Ca 8.9801193858101e-013 O 2.694035815743e-012 -steps -------- svn 3719 -------- Added DELETE keyword to delete any numbered reactant, as listed in the example below. A list of single numbers and number ranges are used to define the reactants to delete from PHREEQC memory. Lists may continue on subsequent lines. Deletion occurs as the last step of simulation calculations, after all other calculations (initial compositions, reactions, transport, inverse modeling) and COPYing have occurred. DELETE -solution 2 3 -equilibrium_phases 2-3 -exchange 2 3 -surface 2-3 -solid_solution 2 3 -gas_phase 2-3 -kinetics 3 2 -mix 2 -mix 3 -reaction 2-3 -temperature 2 3 -------- svn 3704 -------- Added DUMP keyword. Writes complete data for solution, equilibrium_phases, exchange, surface, solid solution, gas phase, and kinetics classes. The format of the output is suitable for data input to the C++ version of PHREEQC. This feature allows the chemical state of a simulation to be saved and read back in as initial conditions for subsequent model runs. Examples: DUMP -all -file myfile.dmp END DUMP -file myfile.dmp -append true -solution 1-2 3 -equi 3 1-2 -exch 1 2 3 -surf 1 2 3 -s_s 1 2-3 -gas 1 -gas 2 -gas 3 -kin 1-3 END Explanation: The first DUMP datablock will write the compositions at the end of the simulation (after all simulation calculations, TRANSPORTs, SAVEs, and COPYs are complete) for every solution, equilibrium_phases, exchange, surface, solid solution, gas phase, and kinetics entities that have been defined or produced in the run. This write includes internally saved entities (usually assigned negative numbers). The second DUMP data appends the compositions of items numbered 1-3 to myfile.dmp, if they exist. The second example shows multiple ways to define the entities to be dumped to file. ------ Begin ------ PHREEQC++ has classes that are equivalent to the PHREEQC C structures. Each class has a method to "dump_raw" the entire set of class data. The lines generated by dump_raw can be read as keyword data blocks in an input file. The following keywords are available in PHREEQC++: SOLUTION_RAW, EQUILIBRIUM_PHASES_RAW, EXCHANGE_RAW, SURFACE_RAW, SOLID_SOLUTIONS_RAW, GAS_PHASE_RAW, and KINETICS_RAW. PHAST uses these classes and data blocks to dump the chemical state of a simulation and read it back in as a starting point for subsequent simulations. Examples of raw output are given below. Some of the fields are required and some are not. SOLUTION_RAW 1 -temp 25 -pH 7 -pe 4 -mu 0.0010001035690258 -ah2o 0.99996599647757 -total_h 111.01243359981 -total_o 55.506216800086 -cb -3.6579285790756e-010 -mass_water 1 -total_alkalinity 3.6579283856577e-010 -totals Cl 0.0010000000000003 H(0) 1.4155655514601e-025 Na 0.0010000000000003 -activities Cl -3.0155266404974 E -4 H(0) -25.15 Na -3.0153891985103 O(0) -42.080029535586 -gammas -Isotopes EQUILIBRIUM_PHASES_RAW 1 -eltList Ba 1 O 4 S 1 -component -name Barite -si 0 -moles 10 -delta 0 -initial_moles 0 -force_equality 0 -dissolve_only 0 -precipitate_only 0 EXCHANGE_RAW 1 Exchange assemblage after simulation 3. -pitzer_exchange_gammas 1 -component -formula X -moles 0 -la 3.0000000302372 -charge_balance 0 -phase_proportion 0 -formula_z 0 -totals Na 1.0000000058717 X 1.0000000058717 -formula_totals X 1 SURFACE_RAW 1 Surface assemblage after simulation 4. -type 2 -dl_type 0 -sites_units 0 -only_counter_ions 0 -thickness 1e-008 -debye_lengths 0 -DDL_viscosity 1 -DDL_limit 0.8 -transport 0 -component -formula Hfo_s -formula_z 0 -moles 0 -la -0.11486188676541 -charge_balance 3.7853465372651e-005 -phase_proportion 0 -Dw 0 -formula_totals Hfo_s 0.01 -totals H 0.01003785346547 Hfo_s 0.010000000000097 O 0.010000000000097 -charge_component -name Hfo -specific_area 600 -grams 1 -charge_balance 3.7853465372651e-005 -mass_water 0 -la_psi 0.55146269389617 -la_psi1 0 -la_psi2 0 -capacitance0 1 -capacitance1 5 -diffuse_layer_totals SOLID_SOLUTIONS_RAW 1 -solid_solution -name Calcite -a0 0 -a1 0 -ag0 0 -ag1 0 -miscibility 0 -xb1 -6.2774385622042e+066 -xb2 -6.2774385622042e+066 -component calcite 0.1 siderite 0.001 GAS_PHASE_RAW 1 -type 0 -total_p 1 -volume 1 -component CO2(g) 1.4305508698401e-005 KINETICS_RAW 1 -step_divide 1 -rk 3 -bad_step_max 500 -use_cvode 0 -cvode_steps 100 -cvode_order 5 -component -rate_name Calcite -tol 1e-008 -m 1 -m0 1 -moles 0 -namecoef CaCO3 1 -d_params 1 1 1 1 -totals -steps ************************************************************ * Features in PHREEQC version 2 not * * documented in WRIR 99-4259. * ************************************************************ ------------------------------------------------------------ Version 2.18.3: April 10, 2011 ------------------------------------------------------------ -------- svn 5570 -------- If -high_precision is set to true in SELECTED_OUTPUT, convergence tolerance is set to 1e-12. If -high_precision is set to false, convergence tolerance is not changed. KNOBS; -convergence_tolerance sets the convergence tolerance to a specified number. The last definition (-high_precision true or -convergence_tolerance) takes precedence for a calculation. ------------------------------------------------------------ Version 2.18.0: April 9, 2011 ------------------------------------------------------------ -------- svn 5212 -------- Added gfm (gram formula mass) as a synonym to gfw in reading concentration data for SOLUTION. S(6) 1 gfm 96 is equivalent to S(6) 1 gfw 96. -------- svn 5170 -------- Added ceil and floor Basic functions. Ceil(x) is the smallest integer greater than or equal to x. Floor(x) is the largest integer less than or equal to x. Note that all numbers in Basic are of type double in C. USER_PRINT 10 print ceil(2.8), floor(2.8), ceil(-2.8), floor(-2.8) This USER_PRINT Basic program has the following output: 3 2 -2 -3 -------- svn 4988 -------- Added EOL$ Basic function. EOL$ is the end of line character for whatever operating system you are running. USER_PRINT 10 PRINT "line 1"+EOL$+"line 2"+EOL$ The result of this USER_PRINT is line 1 line 2 -------- svn 4942 -------- Added additional parameter in PRINT for status. Writing the status line to the screen can slow calculations substantially under some conditions. PRINT -status (t|f|n) t--Print status line. f--Do not print status line. n--Print status line every n milliseconds. -status 1000 would print the status line every second. -------- svn 4830 -------- Changed default for exchange species activty coefficients to be equal to the Pitzer aqueous activity coefficients when using Pitzer aqueous model. Default is -pitzer_exchange_gammas true. ------------------------------------------------------------ Version 2.17.5: September 7, 2010 ------------------------------------------------------------ ------------------------------------------------------------ Version 2.17.4: September 2, 2010 ------------------------------------------------------------ -------- svn 4771 -------- Added synonyms to TOTMOLE: TOTMOL, TOTMOLES ------------------------------------------------------------ Version 2.17.3: August 12, 2010 ------------------------------------------------------------ -------- svn 4191 -------- Added new Basic functions: 10 total_Ca_in_moles = TOTMOLE("Ca") TOTMOLE provides the total number of moles of an element or element valence state in solution. Special values are "water", which gives number of moles of water, and "charge", which gives total equivalents of charge imbalance in solution (same as Basic function CHARGE_BALANCE). In contrast, the Basic function TOT returns moles per kilogram of water, or equivalents per kilogram of water for TOT("charge"). 10 O18_permil = ISO("[18O]") ISO gives an isotopic composition in the input units for an isotope--permil, pmc, or TU in current version of iso.dat. The string argument can be an isotope name, or any item defined in the ISOTOPE_RATIOS data block, For example, ISO("R(13C)_Calcite") will return the carbon-13 composition of the calcite solid solution in permil because of the definitions in iso.dat. 10 D_units$ = ISO_UNITS("D") ISO_UNITS gives the input units for the isotope, D_units$ = "permil" in the example. The string argument can be an isotope name or an item defined in the ISOTOPE_RATIOS data block as explained for the Basic function ISO. ------------------------------------------------------------ Version 2.17.0: February 25, 2010 ------------------------------------------------------------ -------- svn 4006 -------- Changed the calculation of Specific Conductance (SC, uS/cm) to be for the actual temperature of the SOLUTION (in output and in BASIC function SC). Previous versions calculated SC for 25 oC, whereas the complexation model is done at the actual temperature. To obtain SC at 25 oC, use keyword REACTION_TEMPERATURE, for example: SOLUTION 1; K 1; Cl 1; -temp 99 REACTION_TEMPERATURE; 25 END The following example prints to the selected output file the equivalent conductance in (mmho/cm / eq/L) at 20 degrees C for a 1:1 chloride salt solution: USER_PUNCH -head conc eq_EC_20 -start 10 punch tot("Cl"), SC / tot("Cl") * 1e-3 -end where 1e-3 converts from microSiemens/cm to mmho/cm. (The example given with svn 2448 multiplies SC's incorrectly with the ratio of the temperatures.) -------- svn 3986 -------- Added an option for time-substepping in multicomponent diffusion (-multi_D true), keyword TRANSPORT: -time_step 3600 3.0 # 3 time-substeps of 1200 seconds This option is useful to avoid a warning about negative concentrations that may occur in MCD simulations. -------- svn 3902 -------- Added four basic functions for use only with PHAST. The functions are related to the volume, porosity, and water saturation of a PHAST finite-difference cell: CELL_VOLUME--The total volume of the cell in liters. CELL_PORE_VOLUME--The void volume of the cell in liters. CELL_SATURATION--The fraction of the void volume filled with water, unitless. CELL_POROSITY--The porosity of the cell, equal to CELL_PORE_VOLUME / CELL_VOLUME, unitless. For example, in a USER_PUNCH program for a PHAST run, the number of moles of dissolved chloride in a cell is TOT("Cl")*CELL_PORE_VOLUME for confined flow simulations. More generally, the number of moles of dissolved chloride is TOT("Cl")*CELL_SATURATION*CELL_PORE_VOLUME, for confined or unconfined flow. For solids, the number of moles of calcite in the saturated part of a cell is EQUI("Calcite")*CELL_SATURATION*CELL_PORE_VOLUME. For unconfined flow, the solid reactants are distributed between the saturated and unsaturated part of a water- table cell. It is a limitation of PHAST that it is not possible to determine the amounts of solid reactants in the unsaturated part of a cell. Note that for steady-state, unconfined flow, the saturation of cells is constant and the unsaturated part of a water-table cell is never part of the active domain. -------- svn 3600 -------- A new 1/T^2 term (A5 coefficient) was added for all Pitzer-parameter temperature expressions. P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) + A4*(TK*TK - TR*TR) + A5*(1/(TK*TK) - 1/(TR*TR)) where TK is temperature in Kelvin. The optional A5 parameter is read following A4. -------- svn 3591 -------- Added T^2 term to analytical expressions for log k. A T^2 term can now be used in the analytical expressions for any log K. The analytical expression is as follows: log10(K) = A1 + A2*TK + A3/TK + A4*log10(TK) + A5/TK^2 + A6*TK^2, where TK is in Kelvin. The A6 term is the new addition. The optional A6 parameter is read following A5. -------- svn 3485 -------- Added the active fraction model for calculating exchanger compositions described by Appelo (1994), Water Resour. Res. 30, 2793-2805. The active fraction model is useful for calculating the decrease of selectivity when concentrations increase (more specific sites being filled first). In the active fraction model, log(K) of an exchange-half reaction depends on the equivalent fraction on the exchanger: log(K) = log_k + a_f * (1 - ß_i) where log_k is the log of the equilibrium constant when all the sites are occupied by ion i, a_f is an empirical coefficient, and ß_i is the equivalent fraction of i. a_f can be defined in EXCHANGE_SPECIES with -gamma after the WATEQ Debye-Hueckel parameters. Example: EXCHANGE_SPECIES Na+ + X- = NaX; log_k -0.5 -gamma 4.0 0.075 0.50 The association constant for NaX becomes: log(K) = -0.5 + 0.50 * (1 - ß_Na) -------- svn 3453 -------- Added Specific ion Interaction Theory (SIT) activity coefficient model as described in Grenthe, Ingmar, Plyasunov, A.V., and Spahiu, Kastriot, 1997, Estimations of medium effects on thermodynamic data, in Modelling in Aquatic Chemistry, Grenthe, Ingmar, and Puigdomenech, Inasi, eds, OECD Publications, ISBN 92-64-15569-4, 724 p. Implementation is similar to the PITZER implementation, a database with the SIT keyword invokes the SIT activity coefficient model. Currently, No database is provided. The SIT keyword has two identifiers, -epsilon and -epsilon1, where -epsilon gives the pairwise interaction parameters and -epsilon1 gives the linear ionic strength dependency of epsilon, if available. Both parameters allow for temperature dependence with the same expression used in PITZER. The five-term expression for temperature dependence is as follows: P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) + A4*(TK*TK - TR*TR), where TK is Kelvin and TR is 298.15. Example: SIT -epsilon Na+ Br- 0.05 # 0.01 Na+ Cl- 0.03 # 0.01 -epsilon1 # not currently used -------- svn 3288 -------- Additional arguments for the EDL function for the CD_MUSIC surface complexation model. The values of charge, sigma, and psi for the 0, 1, and 2 planes can be obtained from the EDL function. EDL("element", "surface") gives the amount of element in the diffuse layer for "surface". not including sorbed species. "surface" should be the surface name, not the surface-site name (that is, no underscore). Special values for "element" include: "charge" - surface charge, equivalents. For CD_MUSIC "charge" refers to plane 0. "charge1"- surface charge on plane 1, equivalents (CD_MUSIC only). "charge2"- surface charge on plane 2, equivalents (CD_MUSIC only). "sigma" - surface charge density, C/m**2. For CD_MUSIC "sigma" refers to plane 0. "sigma1" - surface charge density on plane 1, equivalents (CD_MUSIC only). "sigma2" - surface charge density on plane 2, equivalents (CD_MUSIC only). "psi" - potential at the surface, Volts. For CD_MUSIC "psi" refers to plane 0. "psi1" - surface charge density on plane 1, equivalents (CD_MUSIC only). "psi2" - surface charge density on plane 2, equivalents (CD_MUSIC only). "water" - mass of water in the diffuse layer, kg. -------- svn 3189 -------- Density of solutions is now calculated from the concentrations of dissolved species. The algorithm has been described by Millero (1974), Millero (2000), Millero (2001) and has been used successfully by Millero and Lepple (1973), Millero et al (1976), Fernendez et al. (1982) and Millero (2000) to calculate the density of seawater, estuaries, lagoons and lakes. The calculation relies on apparent molar volumes phi(i), for individual aqueous species according to the following formula: phi(i) = phi(i,inf) + s(t)I^0.5 + beta(i)I where phi(i,inf) is the apparent molar volume of species i at infinite dilution, s(t) is the Debije-Huckel limiting slope, beta(i) is an empirical constant, and I is the ionic strength. s(t) is calculated as a function of temperature. Parameterizations of phi(i,inf) and beta(i) use the following formulas: phi(i,inf) = a + bt +ct^2 beta(i) = d + et + ft^2 where a, b, c, d, e, and f are empirical constants and t in Celcius. Data input of the constants are in the keyword data block SOLUTION_SPECIES using the new identifier -millero. Example: SOLUTION_SPECIES Na+ = Na+ log k 0.0 -gamma 4.0 0.075 -dw 1.33e-9 -millero -3.46 0.1092 -0.000768 2.698 -0.106 0.001651 Apparent molar volume parameters have been included in the database phreeqd.dat. Calculations made with this database will include the calculated density in the "Description of solution". A new basic function, RHO, can be used to obtain the density in USER_PRINT, USER_PUNCH, and RATES data blocks. Example: USER_PUNCH -heading density 10 PUNCH RHO -------- svn 3183 -------- Added option for an equilibrium-phase to precipitate only, parallel to dissolve_only option. "pre" is added at the end of a line defining an equilibrium- phase. No data fields may be omitted. Should not be used when adding an alternative reaction. Example: EQUILIBRIUM_PHASES Dolomite 0 0.1 dissolve_only Quartz 0 1.5 precipitate_only -------- svn 3160 -------- Surface charge must be higher than -3000 equivalents, when the diffuse double layer composition is calculated with option -donnan. -------- svn 3149 -------- Diffusion through DDL water is multiplied with c_DDL,i / c_i with option -only_counter false. c_DDL,i is the concentration in DDL water, c_i is the concentration in free porewater. (Previous versions used a multiplier of 1). Added -erm_ddl as parameter for aqueous species, to be defined with keyword SOLUTION_SPECIES. erm_ddl (> 0) is an enrichment factor in DDL water calculated with option -donnan: c_DDL,i = c_i * Boltzmann_factor * erm_ddl Example: SOLUTION_SPECIES; Cs+ = Cs+; log_k 0; -erm_ddl 2.1 Default: erm_ddl = 1.0. Added optional multicomponent diffusion of cations in interlayer space of montmorillonite to keyword TRANSPORT. In the example, interlayer diffusion is true (default = false), interlayer porosity is 0.09 (default = 0.1), the porosity where interlayer diffusion stops is 0.01 (default is 0), the tortuosity factor is 150 (default = 100). TRANSPORT -interlayer_D true 0.09 0.01 150 With interlayer_D true, also -multi_D true (and other parameters) must be set, for example: -multi_d true 1e-9 0.3 0.05 1.0 Interlayer diffusion is calculated for the cations associated with X-, defined with keyword EXCHANGE. Mass_transfer = -A * (Dw' / t_f) * c_CEC * grad(beta) A is surface area, A_porewater * (interlayer porosity / free porewater porosity), Dw' is the temperature corrected diffusion coefficient of the aqueous species (defined in SOLUTION_SPECIES), corrected to zero charge transfer, t_f is the interlayer tortuosity factor (-), c_CEC is concentration of total X-, mol(X-) / (L interlayer water). L interlayer water = (L porewater + L DDL- water) * (interlayer porosity / free porewater porosity), grad(beta) is the gradient of the equivalent fraction. -------- svn 2969 -------- Added basic functions that return the activity coefficient of an aqueous species (gamma) and the log base 10 of the activity coefficient of an aqueous species (lg). USER_PUNCH -start 10 punch gamma("H+") # activity coefficient 20 punch lg("H+") # log base 10 activity coefficient -end The functions return zero if the species is not defined for the aqueous model or if the species is an exchange or surface species. ------------------------------------------------------------ Version 2.15.0: February 5, 2008 ------------------------------------------------------------ -------- svn 2680 -------- Identifiers for paramaters controlling the integration by CVODE have been added in the KINETICS data block. -bad_step_max bad_steps -cvode_steps steps -cvode_order order -bad_step_max bad_steps--This option was used only in the Runge-Kutta method. Now, the value of this option is used for CVODE as well. The value entered is the number of times that PHREEQC will invoke CVODE to try to integrate a set of rates over a time interval. Default is 500. -cvode_steps steps--The value given is the maximum number of steps that will taken during one invocation of CVODE. Default is 100. -cvode_order order--CVODE uses a specified number of terms in an extrapolation of rates using the BFD method. Legal values are 1 through 5. A smaller value (2) may be needed if the rate equations are poorly behaved. The default is 5. -------- svn 2457 -------- Added options to inverse modeling to translate current solution definitions in PHREEQC to a Netpath .lon file and (or) to .pat and model files. INVERSE_MODELING -lon_netpath prefix At the beginning of the inverse modeling calculation, each solution that has been defined (or saved) to PHREEQC, is written to the file prefix.lon in a format readable by DBXL (NetpathXL distribution). INVERSE_MODELING -pat_netpath prefix A NETPATH model file is written for each inverse model that is found. The model files are named prefix-n.mod, where n refers to the sequence number of the model. In addition, a file named prefix.pat is written that contains the solutions associated with each model. The solutions are adjusted in accordance with the deltas calculated for the inverse model. Thus, a solution could be used for model 1 and model 2, but the concentrations could be slightly different for the two models. The solutions are identified by an initial integer corresponding to the sequence number of the model, followed by the solution description. -------- svn 2448 -------- Added calculation of specific conductance. Requires the use of phreeqd.dat, which contains the diffusion coefficients of aqueous species. If phreeqd.dat is used, the specific conductance (uS/cm at 25 C) is printed in the "Description of solution". The Basic function SC returns the value of the specific conductance for the solution at 25 C. The following example would print to the selected output file the equivalent conductance in (mmho/cm / eq/L) at 20 degrees C for a 1:1 chloride salt solution: USER_PUNCH -head conc eq_EC_20 -start 10 punch tot("Cl"), SC / tot("Cl") / 1e3 * .89 * 298 / 293 -end where 1e-3 converts from microSiemens/cm to mmho/cm, .89 accounts for the viscosity at 20 C, and 298/293 accounts for the temperature of 20 C. ------------------------------------------------------------ Version 2.14.3: November 17, 2007 ------------------------------------------------------------ -------- svn 2312 -------- Added new option to PITZER datablock, use_etheta t/f. If true, the nonsymmetric mixing terms--cation/cation and anion/anion of different charge--are included; if false these terms are excluded from all equations. Default is true. PITZER -use_etheta true -------- svn 2270 -------- Added additional parameters Pitzer activity formulation for neutral species, MU and ETA. MU applies to nnn, nnn', nn'n'', nna, nn'a, nnc, nn'c interactions, where n, n', and n'' are neutral species, a is an anion and c is a cation. ETA applies to ncc' and naa' interactions. Also modified LAMDA for the special case of nn interactions (coefficients in osmotic and ln equations are different than other interaction types). Source of equations is Clegg and Whitfield, 1991, Activity coefficients in natural waters, Chapter 6, in Pitzer, K.S. (Ed.) Activity Coefficients in Electrolyte Solutions, 2nd Ed. CRC Press, Boca Raton. Removal of the 6 coefficient in last two terms of eq 35 and 36 (p. 2404) per Cleg and Whitfield, 1995, Geochimica et Cosmochemica Acta, v. 59, no. 12, pp 2403-2421. Order of species in definitions should not matter. PITZER -MU CO2 CO2 CO2 ? # nnn CO2 CO2 NH3 ? # nnn' CO2 B(OH)3 NH3 ? # nn'n'' CO2 CO2 Ca+2 ? # nnc CO2 CO2 Cl- ? # nna CO2 NH3 Ca+2 ? # nn'c CO2 NH3 Cl- ? # nn'a -ETA CO2 Ca+2 Mg+2 ? # ncc' CO2 Cl- SO4-2 ? # naa' As with all other Pitzer parameters, a five-term expression for temperature dependence is available: P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) + A4*(TK*TK - TR*TR), where TK is Kelvin and TR is 298.15. A0 through A4 are defined in order. Any undefined values are assumed to be zero. -MU CO2 CO2 CO2 ? ? ? ? ? # nnn ------------------------------------------------------------ Version 2.14.2: September 17, 2007 ------------------------------------------------------------ Fixed logic of memory checking for PhreeqcI. This serious bug makes versions 2.14.0 and 2.14.1 unusable. ------------------------------------------------------------ Version 2.14.1: September 5, 2007 ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.14.0: August 30, 2007 ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.13.3: February 15, 2007 ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.13.2: February 1, 2007 ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.13.1: January 16, 2007 ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.13.0: November 3, 2006 ------------------------------------------------------------ -------- svn 1368 -------- (1) Added multicomponent diffusion (MCD) to transport capabilities. MCD allows different tracer diffusion coefficients for species, but calculates charge balanced transport. In the example, MCD is specified to be true, default tracer diffusion coefficient for species (Dw) is 1e-9, porosity is set to 0.3, porosity limit is set to 0.05, and an exponent of porosity (n) is set to 1.0. Effective diffusion coefficient is defined by the equation: De = Dw * porosity^n. Diffusion stops when the porosity falls below the porosity limit. TRANSPORT -multi_d true 1e-9 0.3 0.05 1.0 Added tracer diffusion coefficient to SOLUTION_SPECIES definitions, -dw identifier. SOLUTION_SPECIES H+ = H+ log_k 0.0 -gamma 9.0 0.0 -dw 9.31e-9 (2) Added phreeqd.dat database with diffusion coefficients (-dw) defined for aqueous species in database directory. (3) Added BASIC functions to obtain and modify the porosity in a cell. The functions can be used in BASIC programs defined with keyword RATES, USER_PRINT, USER_PUNCH and USER_GRAPH. get_por(cell_no) # returns the porosity in cell # 'cell_no' change_por(0.21, cell_no) # porosity of cell 'cell_no' # becomes 0.21 (4) Mobile surface and Donnan option in SURFACE. Mobile surfaces are meant for modeling transport of colloids. Only surfaces with a diffuse double layer can be transported (the ensemble must be electrically neutral). Surfaces related to equilibrium-phases and kinetics cannot be transported. Example 1: Use donnan assumption to calculate the explicit composition of the diffuse layer of surfaces. Thickness of the diffuse layer is defined to be 1e-7 meters. (Default thickness is 1e-8 meters.) Hfo (both sites Hfo_w and Hfo_s) is a surface that is transported with advection and dispersion. The diffusion coefficient of 1e-13 m^2/s is used with option -multi_d true in TRANSPORT. Sfo is an immobile surface (Dw = 0). SURFACE -donnan 1e-7 Hfo_w 97.5e-5 600 88e-3 Dw 1e-13 Hfo_s 2.5e-5 Sfo_w 97.5e-5 600 88e-3 Dw 0 Sfo_s 2.5e-5 Example 2: Define Donnan calculation information. Thickness of the diffuse layer is 1e-8 meters, and relative viscosity is 0.5. Relative viscosity only applies to multicomponent diffusion of solutes in the diffuse layer. (Default viscosity is 1.0.) SURFACE -donnan 1e-8 viscosity 0.5 Example 3: Define Donnan calculation information. Thickness of the diffuse layer is 1.5 Debye lengths, maximum fraction of water that can be in the diffuse layer is 0.9. (Default thickness in Debye lengths is 1, default limit is 0.8.) SURFACE -donnan debye_lengths 1.5 limit_ddl 0.9 When option '-only_counter_ions' is used in conjunction with with '-donnan', all the co-ions (with the same sign of charge as the surface) will be excluded from the DDL, and will be given a concentration of (near) zero in the DDL. (5) Added special BASIC function to change the diffusion coefficient of (part of) a SURFACE, and hence to change the status from mobile to immobile or immobile to mobile. Example 1: take a fraction 0.2 of 'Hfo', rename it to 'Sorbedhfo', with a diffusion coefficient of 0, in cell 'cell_no' USER_PRINT 10 print 'Changing surface in cell ', cell_no 20 change_surf("Hfo", 0.2, "Sorbedhfo", 0, cell_no) Example 2: change the diffusion coefficient of 'Hfo' to 1e-12 m2/s in cell 'cell_no' 10 change_surf("Hfo", 1, "Hfo", 1e-12, cell_no) This function can be used in BASIC programs defined with keywords RATES, USER_PRINT, USER_PUNCH and USER_GRAPH. For correct operation of 'change_surf', the surface components must have been defined with the same surface species (the association constants may differ) and the same diffuse layer thickness or Debye length. The surfaces will be adapted at the end of a calculation step. The result of change_surf does not show up in print or punch results of that step, but the reformatting is effective in the next timestep calculations. -------- svn 1337 -------- Added -add_logk to NAMED_EXPRESSIONS keyword. NAMED_EXPRESSIONS Log_alpha_14C_CO3-2/CO2(aq) -add_logk Log_alpha_14C_CO3-2/CO2(g) 1 -add_logk Log_alpha_14C_CO2(aq)/CO2(g) -1 -------- svn 1281 -------- Added new option to PITZER data block to allow definition of alpha1 and alpha2 for specific electrolytes. Entries are following -ALPHAS are Ion1, Ion2, alpha1, alpha2. Both alpha1 and alpha2 should be defined. Default is 0.0 for undefined values following Ion1 and Ion2. Example: PITZER -ALPHAS # # Defaults for ion valences in salts # # 1-N (only B1): alpha1 = 2 # 2-2: alpha1 = 1.4 alpha2 = 12.0 # 3-2, 4-2: alpha1 = 2 alpha2 = 50 # #Ion1 Ion2 Alpha1 Alpha2 Fe+2 Cl- 2 1 Fe+2 SO4-2 1.559 5.268 -------- svn 1279 -------- Added new Basic function OSMOTIC that returns the osmotic coefficient if the Pitzer model (PITZER keyword data block) is used or 0.0 if the ion-association model is used. Example: USER_PRINT 10 PRINT "Osmotic coefficient: ", OSMOTIC -------- svn 1245 -------- Enabled redox in Pitzer model with option in PITZER keyword. Typically, the option will be included in the pitzer database file. Example: PITZER -redox TRUE The default database for the Pitzer model does not contain any redox definitions and the default value for the option is FALSE. At a minimum, species O2 and H2 must be defined in the database or input file to allow redox calculations. -------- svn 1207 -------- Added option to force an equilibrium phase to be included in the equality constraints. Normally, the SIs of equilibrium phases are optimized to be negative and the sum of SIs is minimized. If -force_equality is used, then the phase must reach its target SI or the calculation fails with an error. Example: EQUILIBRIUM_PHASES Fix_pH -7 NaOH -force_equality Calcite 0 Dolomite 0 CO2 -3.5 One example of using the new option would be to ensure that a target pH is attained, as in the example above. -------- svn 1179 -------- New option (-sites_units or -sites) allows alternative units (sites/nm^2) for definition of number of sites for a surface. This approach requires better consistency among the parameters as both the number of sites and the surface area are based on the mass. It makes more sense than the default, which requires the number of sites (first numeric item in a line) to be defined in units of moles, independently of the number of grams of sorbent. Units descriptor is either DENSITY, for defining number sites/nm^2, or ABSOLUTE, for defining number of sites in moles. Optionally, sites, sites_units, or -s[ites_units]. ABSOLUTE is the default for backward compatibility with input files. Example: SURFACE 1 -sites_units DENSITY SurfOH 2.6 600. 1.0 SurfaOH 2.6 30. 2.0 Explanation: In this example, Surf has a site density of 2.6 sites per nanometer squared, a specific area of 600 meters squared per gram, and a mass of 1 gram. Surfa has a site density of 2.6 sites per nanometer squared, a specific area of 30 meters squared per gram, and mass of 2 grams. -------- svn 1096 -------- Allows solids and gases in the equations for PHASES. This capability simplifies the definitions for gas and solid isotopic components. Solids must be identified with "(s)" and gases with "(g)". The first entity on the left- hand-side of the equation must be the stoichiometric formula of the solid or gas component being defined, optionally with (g) or (s). In turn gases and solids included in the equation must be defined with reactions that ultimately allow the defined species (C[18O]2(g) in this case) in terms of aqueous species. Example: PHASES C[18O]2(g) C[18O]2(g) + CO2(g) = 2CO[18O](g) log_k 0.602059991327962396 # log10(4) -------- svn 1092 -------- CD_MUSIC sorption model has been implemented. Still missing logic for surfaces related to equilibrium- phases and kinetics. Has explicit calculation of diffuse layer composition with Donnan assumption. Old diffuse-layer calculation will not be implemented. Example: SURFACE Goe_uniOH .000552 96.387 1 -capacitance 1.1 5 Goe_triO .000432 -cd_music -donnan Explanation: 1.1 5 are capacitances for the cd-music model for 0-1 and 1-2 planes, respectively. -cd_music specifies that the surface is a cd-music surface. -donnan optionally calculates the diffuse layer composition with the Donnan model. Example: SURFACE_SPECIES Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O log_k 20.1 # eq 7 K1, Kin1 -cd_music -1 -6 0 0.25 5 Explanation: -cd_music--this option is used to specify the change in charge by the reaction for three planes, 0 (specific sorption at the surface), 1 (Stern layer), and 2 (or d, the diffuse layer). The five numbers in the form above are (1) the change in charge for plane 0 due to loss or gain of hydrogen and oxygen at plane 0, (2) the change in charge for plane 1 due to the hydrogen and oxygen in the ligand that are located at plane 1, (3) the change in charge in diffuse layer, plane 2, (4) the fraction of the central ion charge that is associated with plane 0, and (5) the charge on the central ion. In this example the change in charge at plane 0 is (delta z0) = -1 (loss of one hydrogen) + 0.25*5 (contribution from As+5) = 0.25. The charge at plane 0 becomes -0.5 + 0.25 = -0.25. The change in charge at plane 1 is (delta z1) = -6 (3 oxygens of the ligand are located at plane 1) + (1-0.25)*5 (contribution from As+5) = -2.25. The charge at plane 1 becomes 0 + (-2.25) = -2.25. There is no change in charge associated with plane 2. The total charge of the species is -0.25 (plane 0) + -2.25 (plane 1) + 0 (plane 2) = -2.5. Alternatively to the form above, the changes in charge on the three planes can be entered directly as the first three numbers in the option, followed by two zeros. Thus, the following is equivalent to the -cd_music definition above, and consistent with more recent papers which would list delta z0 = 0.25, delta z1 = -2.25 and delta z2 = 0: SURFACE_SPECIES Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O log_k 20.1 # eq 7 K1, Kin1 -cd_music 0.25 -2.25 0 0 0 -------- svn 675: -------- Added PRINT option to print the species that contribute to alkalinity. Alkalinity distribution is printed in the output file following the distribution of species. Default at program startup is false. Example: PRINT -alkalinity true ------------------------------------------------------------ Version 2.12: ------------------------------------------------------------ * Made aqueous activity coefficients the default activity coefficients for exchange species when using the Pitzer formulation. New option in EXCHANGE is -pitzer_exchange_gammas T/F, default is true; defining "false" sets exchange activity coefficients to 1.0. Option has no effect for ion-association model (non-Pitzer). * Added multiplier format to REACTION steps and KINETICS steps, which simplifies definition of multiple equal reaction increments. This definition: INCREMENTAL_REACTIONS true REACTION H2O 1 -36 3*-4 2*-.25 -0.19 4*-0.1 3*-0.05 moles is equivalent to this definition: INCREMENTAL_REACTIONS true REACTION H2O 1 -36 -4 -4 -4 -.25 -.25 -0.19 -0.1 -0.1 -0.1 -0.1 -0.05 -0.05 -0.05 moles * Added Pitzer activity formulation. Use pitzer.dat database to invoke the Pitzer model. Should have same capabilities as ion-association model except explicit diffuse layer calculation is not implemented with the Pitzer model. New keyword is PITZER with following options: PITZER -MacInnes T/F # uses MacInnes assumption or unscaled for # individual activities and activity coefficients -B0 Na+ Cl- 0.0765 -777.03 -4.4706 0.008946 -3.3158E-6 -B1 Na+ Cl- 0.2664 0 0 6.1608E-5 1.0715E-6 -B2 Mg+2 SO4-2 -37.23 0 0 -0.253 -C0 Na+ Cl- 0.00127 33.317 0.09421 -4.655E-5 -THETA K+ Na+ -0.012 -LAMDA Na+ CO2 0.1 -ZETA H+ Cl- B(OH)3 -0.0102 -PSI Na+ K+ Cl- -0.0018 A five-term expression for temperature dependence is available for all Pitzer parameter values: P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) + A4*(TK*TK - TR*TR), where TK is Kelvin and TR is 298.15. * Cl1mp is a new multiple precision version of routine cl1, a simplex-based optimization routine. Cl1mp was develeped by using the Gnu Multiple Precision package (gmp). Calculations are carried out to about 30 significant digits. Cl1mp may help in some situations where roundoff errors are a problem, but it is still possible that roundoff errors will cause cl1mp to fail to find a solution to an optimization problem. The mp version has the following options in INVERSE_MODELING: -multiple_precision T/F--causes the mp version to be used in inverse modeling calculations. -mp_tolerance 1e-12--tolerance for mp version of cl1. As in cl1, numbers less than the tolerance are considered to be zero. 1e-12 is the default. -censor_mp 1e-20--as calculations occur in the linear equation array, elements less than this value are set to zero. Default is 1e-20. A value of 0.0 causes no censoring to occur. ------------------------------------------------------------ Version 2.11: ------------------------------------------------------------ * A new database, minteq.v4.dat, has been translated from version 4.02 of MINTEQA2 and is included in all distributions. The database minteq.dat from earlier version of MINTEQA2 has been slightly revised and is also included. ------------------------------------------------------------ Version 2.10: ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.9: ------------------------------------------------------------ * Added new keyword COPY that allows a data entity to be copied from one index to a new index or to a range of indicies. Format is COPY keyword index index_start[-index_end] where keyword may be SOLUTION EQUILIBRIUM_PHASES EXCHANGE GAS_PHASE KINETICS MIX REACTION REACTION_TEMPERATURE SOLID_SOLUTION SURFACE * Added new Basic functions b$ = PAD(a$, 20) pads a$ to a total of 20 characters with spaces and stores result in b$. PAD returns a copy of a$ if a$ is more than 20 characters. i = INSTR(a$, b$) sets i to the character position of string b$ in a$, 0 in not found. b$ = LTRIM(a$) trims white space from beginning of string a$ and stores result in b$. b$ = RTRIM(a$) trims white space from end of string a$ and stores result in b$. b$ = TRIM(a$) trims white space from beginning and end of string a$ and stores result in b$. * Added new Basic function SYS that calculates the total amount of an element in all phases (solution, equilibrium_phases, surfaces, exchangers, solid solutions, and gas phase). KINETIC reactions are not included. The function has two forms: (1) one element name as an argument (variable names are user specified) 10 t = SYS("As") the function will return the total arsenic in the system. (2) 5 argumens 10 t = SYS("As", count_species, names$, types$, moles) will return the total arsenic in the system to t; count_species-- the number of species that contain arsenic, including solution, equilibrium_phases, surfaces, exchangers, solid solutions, and gas phase species; names$--a character array that has the name of each species; type$--a character array that specifies the type of phase for the species, aq, equi, surf, ex, s_s, gas, diff. Diff refers to the amount of the element in the diffuse layer of a surface when the explicit diffuse layer calculation is used; moles--an array containing the number of moles of the element in the species. The sum of moles(i) is equal to tot. SYS has several special arguments for the form SYS("arg", count, names$, types$, values) arg is one of the options listed below. count is a single numeric value and is the number of elements in the following arrays. name$ is an array of string values. type$ is an array of string values. values is an array of numeric values. Values of arg: elt_name returns total number of moles of element in system. count is the number of species for the element in the system, including aqueous, exchange, surface, equilibrium_phase, solid solution component, and gas phase "species". Arrays are filled for each "species"; values are moles. "elements" returns total number of moles of dissolved elements other than H and O. count is number of elements, valence states, exchangers, and surfaces. Arrays are filled for each element and valence state, type is "dis"; exchanger, type is "ex", and surface, type is "surf". Values are moles. "phases" returns maximum saturation index of all phases. count is number of phases in system. Arrays are filled for each phase; values are saturation indexes. "aq" returns sum of moles of all aqueous species. count is number of aqueous species in system. Arrays are filled with each aqueous species; values are moles. "ex" returns sum of moles of all exchange species. count is number of exchange species in system. Arrays are filled with each exchange species; values are moles. "surf" returns sum of moles of all surface species. count is number of surface species in system. Arrays are filled with each surface species; values are moles. "s_s" returns sum of moles of all solid solution components. count is number of solid solution components in system. Arrays are filled with each solid solution component; values are moles. "gas" returns sum of moles of all gas components. count is number of gas components in system. Arrays are filled with each gas component; values are moles. * Added new Basic function, DESCRIPTION, that has the value defined for the description field of the SOLUTION keyword line. * Added alternative ordinary differential equation solver called CVODE, a set of C routines from the Lawrence Livermore National Labs. CVODE is part of the SUNDIALS package. CVODE is used in place of the Runge Kutta method when "-cvode true" is used within a KINETICS data block. KINETICS -cvode true ------------------------------------------------------------ Version 2.8: ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.7: ------------------------------------------------------------ Changed format of selected output file: Removed quotations surrounding strings in headings. Removed quotations surrounding strings in state variable. All fields are 12 or 20 places depending on -high_precision. Headings are not truncated even if longer than specified precision. For isotopes, missing value is -9999.9 Selected output is updated each simulation. If a species or phase is defined subsequent to the simulation where SELECTED_OUTPUT was defined it will appear in the selected output file in the simulation in which it is defined and in subsequent simulations. Added strings for each file, which can be extracted from the executable file with the "ident" command. Fixed null pointer for isotope_ratios if Basic routine was undefined. Fixed problem in C++ if structure name is same as member name. logk member of logk structure was renamed to log_k. Added identifier -add_constant to PHASES, EXCHANGE_SPECIES, SOLUTION_SPECIES, and SURFACE_SPECIES. -add_constant -0.301 log K is augmented by the specified constant. Theory and implementation of isotopes in PHREEQC is documented in: Thorstenson, D.C., and Parkhurst, D.L., 2002, Calculation of individual isotope equilibrium constants for implementation in geochemical models: U.S. Geological Survey Water-Resources Investigations Report 02-4172, 129 p. Added KEYWORDS: ISOTOPES Element -isotope isotope_name units standard_ratio -total_is_major T/F (OPTION IS DISABLED!!) CALCULATE_VALUES Name -start Basic statements, must have SAVE -end ISOTOPE_RATIOS (for printing) Name=Calculate_values_name Isotope_name ISOTOPE_ALPHAS (for printing) Name=Calculate_values_name Named_logk=named_expression_name Basic functions: calc_value("calc_value_name") evaluates a definition of CALCULATE_VALUES lk_named("name") log10(K) of definition in NAMED_EXPRESSIONS lk_phase("name") log10(K) of definition in PHASES lk_species("name") log10(K) of definition in (SOLUTION, EXCHANGE, SURFACE)_SPECIES sum_gas("template","element") Sum of element in gases with specified template, moles. Example: template="{C,[13C],[14C]}{O,[18O]}2" includes all CO2 gases sum_species("template","element") Sum of element in aqueous, exchange, and surface species with specified template (moles) sum_s_s("s_s_name","element") Sum of element in a specified solid solution (moles) PRINT keyword: -initial_isotopes T/F -isotope_ratios T/F -isotope_alphas T/F -censor_species 1e-8 # omit species from Distribution of Species if less than # relative minimum of an element or element redox state # total concentration SELECTED_OUTPUT keyword: -calculate_values name1 name2 ... -isotopes minor_isotope1 minor_isotope2 .... Added functions LK_SPECIES, LK_NAMED, LK_PHASE for Basic interpreter. LK_SPECIES("CaHCO3+") returns the log k for the association reaction for the ion pair CaHCO3+ at the current temperature. The log K is for the reaction as defined in the database or input file. Similarly, LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)") returns the value for the log K at the current temperature using expressions defined in NAMED_LOG_K data block; LK_PHASE("Calcite") returns the value of log K for calcite at the current temperature for the dissociation reaction defined in the database or input file. Values are "log10" values. Example for Basic program: 10 PRINT "Log10 KCalcite: ", LK_PHASE("Calcite") 20 PRINT "Log10 KCaHCO3+: ", LK_SPECIES("CaHCO3+") 30 PRINT " 1000ln(alpha): ", LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)")*LOG(10)*1000 NAMED_EXPRESSION--New keyword data block. This data block was implemented to facilitate isotopic calculations. It allows analytical expressions that are functions of temperature to be defined. The purpose is to separate the fractionation factors from the log K, so that the fractionation factor or its temperature dependence can be easily modified. The named expression can be added to a log K for a species or phase by the -add_logk identifier in SOLUTION_SPECIES EXCHANGE_SPECIES, SURFACE_SPECIES, or PHASES data block. Log K, Delta H, and analytical expressions for a log K can be defined with identifiers -log_k, -delta_h, and -analytical_expression as described in SOLUTION_SPECIES in WRIR 99-4259. Fractionation factors are often defined as 1000*ln(alpha). The identifier -ln_alpha1000 can be used to enter data in this form. The analytical expression is the same as defined in SOLUTION_SPECIES, but the result of the expression is converted to log10(alpha) by dividing by 1000*ln(10) before it is summed into log K values. NAMED_EXPRESSIONS Log_K_calcite # CaCO3 + 2H3O+ = Ca+2 + 3H2O + CO2 log_k 8.201 delta_h -8.035 kcal -analytic 292.29 0.015455 -24146.841 -94.16451 2248628.9 Log_alpha_18O_CO2(aq)/Calcite -ln_alpha1000 3.8498 0.0 10.611e3 0.0 -1.8034e6 Log_alpha_13C_CO2(aq)/Calcite -ln_alpha1000 2.72 0.0 0.0 0.0 -1.1877e6 ------------------------------------------------------------ Added identifier -add_logk to SOLUTION_SPECIES EXCHANGE_SPECIES, SURFACE_SPECIES, and PHASES data block. Allows a named expression to be added to the definition of the log K for a species or phase. In the following example, the log K for the phase Ca[14C][18O]3 is summed from four parts, one defined with the log_k identifier and the other three parts from expressions defined in NAMED_EXPRESSIONS. The named expression is multiplied by the coefficient at the end of the line before it is summed into the log K. A missing coefficient is 1.0 by default. PHASES Ca[13C][18O]3 Ca[13C][18O]3 + 3CO2 + 2H3O+ = Ca+2 + 3H2O + 3CO[18O] + [13C]O2 log_k 0.903089986991 # 3*log10(2) -add_logk Log_K_calcite 1.0 -add_logk Log_alpha_13C_CO2(aq)/Calcite 1.0 -add_logk Log_alpha_18O_CO2(aq)/Calcite 3.0 SOLUTION keyword: At present, can only define isotopes in the units defined in ISOTOPES. ------------------------------------------------------------ Version 2.6: ------------------------------------------------------------ No new features. ------------------------------------------------------------ Version 2.5: ------------------------------------------------------------ Added the capability to use square brackets to define an "element" name. The brackets act like quotation marks in that any character string can be used within the brackets as an element name. For example, [Fe3], [13C], and [N5] are now legal "element" names. All element names without brackets must begin with a capital letter, followed by zero or more lower case letters and underscores. Added identifier -activity_water for a species in SOLUTION_SPECIES data block. This identifier has been added for future updates that will allow isotopic calculations. It is intended to be used only for isotopic variations of H2O, like D2O or H2[O18]. It forces the activity coefficient for the species to be activity(water)/55.5. This effectively sets the activity of the species to the mole fraction in solution. Added identifier -bad_step_max to KINETICS data block. An integer following -bad_step_max gives the maximum number of times a rate integration may fail before execution of the program is terminated. Default is 500. ------------------------------------------------------------ Version 2.4: ------------------------------------------------------------ ------------------------------------------------------------ Added identifier -warnings to PRINT keyword. An integer following -warnings gives the maximum number of warnings to print into the output file. A negative number allows all warnings to be printed. Example: -warnings 20 ------------------------------------------------------------ Changed the results of the function CELL_NO in Basic programs. Function cell_no in Basic now prints a number equivalent to -solution in SELECTED_OUTPUT data block. It gives the solution number for initial solution calculations and the solution being used in batch reaction calculations. Result is the same as previous versions for ADVECTION or TRANSPORT calculations. ------------------------------------------------------------ Version 2.3: ------------------------------------------------------------ DATABASE--New keyword data block It must be the first keyword in the input file. The character string following the keyword is the pathname for the database file to be used in the calculation. The file that is specified takes precedence over any default database name, including environmental variable PHREEQC_DATABASE and command line arguments. LLNL_AQUEOUS_MODEL_PARAMETERS--New keyword data block Added new keyword to make aqueous model similar to EQ3/6 and Geochemists Workbench when using llnl.dat as the database file. Values of Debye-Huckel a and b and bdot (ionic strength coefficient) are read at fixed temperatures. Linear interpolation occurs between temperatures. New options for SOLUTION_SPECIES are -llnl_gamma a , where a is the ion-size parameter. -co2_llnl_gamma , indicates the temperature dependent function for the bdot term given in -co2_coefs of LLNL_AQUEOUS_MODEL_PARAMETERS will be used. Applies to uncharged species only. LLNL_AQUEOUS_MODEL_PARAMETERS -temperatures 0.0100 25.0000 60.0000 100.0000 150.0000 200.0000 250.0000 300.0000 #debye huckel a (adh) -dh_a 0.4939 0.5114 0.5465 0.5995 0.6855 0.7994 0.9593 1.2180 #debye huckel b (bdh) -dh_b 0.3253 0.3288 0.3346 0.3421 0.3525 0.3639 0.3766 0.3925 -bdot 0.0394 0.0410 0.0438 0.0460 0.0470 0.0470 0.0340 0.0000 #cco2 (coefficients for the Drummond (1981) polynomial) -co2_coefs -1.0312 0.0012806 255.9 0.4445 -0.001606 ------------------------------------------------------------ Added function SURF to Basic. SURF("element", "surface") gives the amount of element sorbed on "surface". "surface" should be the surface name, not the surface-site name (that is, no underscore). ------------------------------------------------------------ Allow decimals in definition of secondary master species. Some redox states do not average to integers, for convenience in identifying them, decimal numbers may be used within the parentheses that define the redox state, example S(0.3) could be used in the MASTER_SPECIES data block for the valence state of aqueous species S6-2. ------------------------------------------------------------ Eliminate echo of input file in PRINT data block. -echo_input T/F turns echoing on and off. Default is true, initial value is true. ------------------------------------------------------------ Added option for an equilibrium-phase to dissolve only. "dis" is added at the end of a line defining an equilibrium- phase. No data fields may be omitted. Should not be used when adding an alternative reaction. Example: EQUILIBRIUM_PHASES Dolomite 0.0 0.001 dis ------------------------------------------------------------ Version 2.2: ------------------------------------------------------------ Added function EDL to Basic. EDL("element", "surface") gives the amount of element in the diffuse layer for "surface", not including sorbed species. "surface" should be the surface name, not the surface-site name (that is, no underscore). Special values for "element" include: "charge" - gives surface charge, equivalents. "sigma" - surface charge density, C/m**2. "psi" - potential at the surface, Volts. "water" - mass of water in the diffuse layer, kg. ------------------------------------------------------------ End of Features not documented in WRIR 99-4259. ------------------------------------------------------------ ************************************************************ ************************************************************ * Revisions and Bug Fixes * ************************************************************ ************************************************************ ------------------------------------------------------------ Version 3.1.6: January 20, 2015 ------------------------------------------------------------ -------- svn 5570 -------- In SELECTED_OUTPUT; -totals, a redox state defined with a "+" sign, such as Fe(+3), was not recognized ("Fe(3)" worked correctly). Now Fe(+3) is synonymous with Fe(3). ------------------------------------------------------------ Version 2.18.0: April 9, 2011 ------------------------------------------------------------ -------- svn 5212 -------- Subscript error in solver (ineq) when reseting deltas after optimization failed. -------- svn 4996 -------- Had conversion conversion to Kelvin as 273.16 in Basic function TK, should be 273.15. -------- svn 4955 -------- Changed O2(g) constant in Amm.dat and iso.dat to definition from llnl.dat. -------- svn 4954 -------- Added two more parameter sets in series of attempts to converge: tolerance/100 and tolerance/1000. -------- svn 4943 -------- Added separate As(3) in sit.dat. -------- svn 4854 -------- Added two additional convergence parameter sets: ineq_tol/100 and ineq_tol/1000. -------- svn 4840 -------- Added missing -dw parameters to MgCO3, MgHCO3, and MgSO4 aqueous species in phreeqc.dat. ------------------------------------------------------------ Version 2.17.5: September 7, 2010 ------------------------------------------------------------ -------- svn 4793 -------- Revised fix for exponential of negative number in Basic. Error message for negative number raised to a fractional power. ------------------------------------------------------------ Version 2.17.4: September 2, 2010 ------------------------------------------------------------ -------- svn 4771 -------- Added synonyms to TOTMOLE: TOTMOL, TOTMOLES Fixed bug with negative exponential in basic, for example -0.006^0.9 ------------------------------------------------------------ Version 2.17.3: August 12, 2010 ------------------------------------------------------------ -------- svn 4727 -------- Increased maximum iterations in cl1 solver. One test case failed after new compiler was installed. -------- svn 4700 -------- Initialized (nearly) all variables in class. -------- svn 4697 -------- Fixed bug with second PITZER data block, parameters were not updated if temperature was not changed. -------- svn 4698 -------- Modified PHRQ_malloc and PHRQ_free logic. These routines are used in almost all cases. -------- svn 4694 -------- Initialized variables for V_M structure, rxn->dz (for CD_MUSIC), Fixed problem where definitions in second SIT data block were not added to model. -------- svn 4677 -------- Renamed all variables that "shadowed" class variables. -------- svn 4643 -------- Made isfinite a macro. -------- svn 4539 -------- Fixed bug with long file names in inverse modeling files netpath.fil or model.fil. -------- svn 4490 -------- Redox had never been enabled for the SIT formulation. Added the switch to include the hydrogen balance equation for SIT. -------- svn 4458 -------- Tweaked the convergence parameters for Pitzer log gamma unknowns. Set a maximum step size for these unknowns. Also changed usage of internal flags for Pitzer calculations related to initial solution calculations. Corrected print of Gamma iterations. -------- svn 4399 -------- Error in PHRQ_calloc. Size of allocated block was not set. Under some situations, could cause serious errors and a crash. -------- svn 4376 -------- Error in logic for removing unstable phases for Pitzer and SIT. -------- svn 4233 -------- Removed duplicate parameter for Na+ -- Cl- in sit.dat. Value of 0.03 was entered erroneously for both Na/Cl and Cl/Na. ------------------------------------------------------------ Version 2.17.0: February 25, 2010 ------------------------------------------------------------ -------- svn 4115 -------- Fixed bugs with unititialized strings in Basic, which caused an error in renumbering with PhreeqcI. Tested most Basic functions. Fixed bugs with LG and GAMMA functions, which did not return the correct values for H+. GET_POR now returns 0 if it is not a TRANSPORT calculation. -------- svn 4066 -------- Fixed bug with SIT calculations (and Pitzer). The number of solver iterations was too few (200). With SIT and Pitzer, each species has an unknown, so the number of unknowns is large for a system with many elements. Now set the maximum iterations to be equal to the number of unknows plus the number of equations/inequalities. -------- svn 4023 -------- Trapped error when -mole_balance option was used in SOLUTION_SPECIES and one of the stated elements was not defined. -------- svn 4022 -------- Redefined CN- and SCN- to be new elements Cyanide and thiocyanate in llnl.dat. Former definitions were not useful because cyanide and thiocyanate were never stable and defining a master species as CN- caused problems with mole balances, appearing in solutions without any carbon. -------- svn 3901 -------- Error with equations that included (s) or (g). The equation and log K were correct only for the simulation when initially read. Now equations an log Ks are correct for all simulations. Calculates saturation index from the equation after (s) and (g) are eliminated. -------- svn 3695 -------- For transport calculations, fixed step_fraction when nmix == 1 and ishift == 0. -------- svn 3684 -------- Added more precision in writing dump file fields. Multiple REACTIONS were not sorted correctly. Added sort routine to tidy.c. -------- svn 3640 -------- Print correct temperature for gas phase dump. Correct total moles of exchanger for function sys("X"). -------- svn 3568 -------- minteq.dat: Changing log K of gypsum to minteq version 4 value (-4.61). Old value (-4.848) is too stable. -------- svn 3483 -------- Alkalinity is now printed to the selected output file when the Alkalinity is used with -totals. SELECTED_OUTPUT; -totals Alkalinity Modified numerical method to attempt to produce a numerical solution when complexes are extremely strong. llnl.dat As and F complexes caused PHREEQC to fail on an initial solution calculation. The terms of the As and F mass balance equations were identical to machine precision. One unknown log activity was adjusted but the other was not. Now attempts an adjustment for the unadjusted log activity. -------- svn 3463 -------- Modified handling of not-a-number in places that affected the adjustment of log activities (reset and revise guesses). Uses isfinite function that is available on Linux and is ifdef'd in global.h for Visual Studio. The NaN problem occurred rarely and was related to bad results from the solver and when poor estimates were available in revise_guesses. Also insured that log activity for new master species was well defined in switch_bases. -------- svn 3446 -------- Fixed errors in casting for long double version. -------- svn 3440 -------- Adjusted numerical calculation to avoid extremely large calculated specific conductances in high ionic strength waters. -------- svn 3433 -------- -dw and -millero added to phreeqc.dat, which allows calculation of specific conductance and density. phreeqd.dat is now redundant and removed from distribution. -------- svn 3425 -------- Added error message to require -multi_d for transport of surfaces. -------- svn 3424 -------- Checked for misspellings in EXCHANGE definitions, which previously caused crash. -------- svn 3423 -------- -dw and -millero added to pitzer.dat, which allows calculation of specific conductance and density. -------- svn 3292 -------- Removed redundant warnings related to transport of exchanger and surface. -------- svn 3287 -------- Fixed error in CD_MUSIC surface complexation model. If reaction equation for a surface species was not written with the primary surface species, the calculation was incorrect. The logic to accumulate the change in charges on the planes was erroneously not included when rewriting the equations to the master species. -------- svn 3247 -------- Revised donnan layer calculation with CD_MUSIC. Fixed a bug related to moles versus concentration and stream lined calculation. Minor differences in relevant test cases. -------- svn 3207 -------- Modifications to convergence criteria for surfaces related to minerals, when moles of mineral is near zero (<= 1e-14). -------- svn 3100 -------- Error when multiple surfaces were used. Sometimes the surface area from one surface was used for another. Results were probably incorrect if the surfaces were not in alphabetical order in their definition in SURFACE. -------- svn 2711 -------- Cleaned up compiler warnings for functions called with constant strings. ------------------------------------------------------------ Version 2.15.0: February 5, 2008 ------------------------------------------------------------ -------- svn 2386 -------- Fixed bug for SELECTED_OUTPUT; -activities H2O. The resulting value was -30; now produces the correct result. ------------------------------------------------------------ Version 2.14.3: November 17, 2007 ------------------------------------------------------------ -------- svn 2386 -------- Fixed bug in routine find_Jstag. Incorrect index (cell_no) caused segmentation violation in rare instances. -------- svn 2312 -------- Added new option to PITZER datablock, use_etheta t/f. -------- svn 2279 -------- Error lost 200 moles of mineral. Should only be a problem in some cases where moles of mineral is greater than 200. -------- svn 2270 -------- Added additional parameters Pitzer activity formulation for neutral species, MU and ETA. -------- svn 2269 -------- Fixed buffer overrun in SOLUTION_SPREAD when pasting. -------- svn 2268 -------- Fixed error in prep.c where realloc was called instead of PHRQ_realloc, which eliminated a memory leak. ------------------------------------------------------------ Version 2.14.2: September 17, 2007 ------------------------------------------------------------ -------- svn 2267 -------- Fixed logic of memory checking for PhreeqcI. This serious bug makes versions 2.14.0 and 2.14.1 unusable. ------------------------------------------------------------ Version 2.14.1: September 5, 2007 ------------------------------------------------------------ -------- svn 2219 -------- Updated transport.c to adjust transport in diffuse layer to be charge balanced for MCD calculation. ------------------------------------------------------------ Version 2.14.0: August 30, 2007 ------------------------------------------------------------ ------------- svn 2203-2204 ------------- Revised logic for using phqalloc memory checker. Compiler option USE_PHRQ_ALLOC now turns on memory checker. If USE_PHRQ_ALLOC is defined and NDEBUG is not defined, file name and line number are also used in memory checking. Model.c now uses same compile options as all other files. -------- svn 2199 -------- Initialized variables that caused problems when rerunning simulations in PfW and PhreeqcI. -------- svn 2138 -------- Fixed bugs in MCD calculation related to saving solutions after initialization. -------- svn 2055 -------- Profiled and optimized of code. Automatic string in Basic factor saves many mallocs. Reordered to minimize call to strcmp_nocase in basicsubs.c and xsolution_save. Minimized mallocs for solver. -------- svn 2051 -------- Fixed bugs in MCD calculation. -------- svn 2040 -------- Fixed warnings for type-punned with new gcc. Reverted to 2.12 for infilling solutions for transport. Only solutions are used, not additional reactants for solution 0 and n+1. Added digits to printout of REACTION stoichiometry. -------- svn 1852 -------- Fixed error in CDMUSIC surface related to a phase. Stoichiometry of H was calculated incorrectly. -------- svn 1837 -------- Initialize flag for MCD calculation. PhreeqcI would do MCD calculation after TRANSPORT was redefined not to do MCD calculation. ------------------------------------------------------------ Version 2.13.2: February 1, 2007 ------------------------------------------------------------ -------- svn 1700 -------- Fixed bug with redox elements in multi_diffusion stagnant zones. -------- svn 1683 -------- Worked on convergence problems when optimizer fails to find a solution. Censored values greater than 1e8. -------- svn 1637 -------- Fixed bug with dissolve only in ADVECTION calculations. -------- svn 1629 -------- Fixed bug with redox elements in multi_diffusions. Added Phreeqc For Windows changes from 2.13.1. ------------------------------------------------------------ Version 2.13.1: January 16, 2007 ------------------------------------------------------------ -------- svn 1600 -------- Fixed logic error that required rebuilding aqueous model when not necessary. Now runs faster (sometimes 3X) than version 2.13.0. -------- svn 1590 -------- Removed porosity from one statement to eliminate oscillations in multicomponent diffusion calculation. -------- svn 1558 -------- Dissolve-only option did not work correctly for stagnant cells in TRANSPORT calculations. The moles of equilibrium phases, kinetics, gas_phase, and solid solutions were not initialized at the beginning of each transport step. Thus, the printed values for delta moles for the step in the output and punch file were incorrect for stagnant-zone cells. "Dissolve only" was always tested relative to the number of moles initially in the cells, not the amount remaining at a given time step. -------- svn 1485 -------- Pitzer version with gas_phase did not work. Added gas_phase and cd_music to numerical derivative routine. svn 1368: (1) Added multicomponent diffusion in transport and SOLUTION_SPECIES. (2) Added BASIC functions to obtain and modify the porosity in a cell. (3) Aded mobile surface and Donnan option in SURFACE. (4) Added special BASIC function to change the diffusion coefficient of a SURFACE, and hence to change the status from mobile to immobile or immobile to mobile. svn 1337: Added -add_logk to NAMED_EXPRESSIONS keyword. svn 1306: Revised printing of distribution of species, pure phase assemblages, and solid solutions to use longer fields for names. More revisions to logic for using gases and solids in equations for phases. Revised logic for solid solutions with small (1e-25) amounts of component. svn 1282: Fixed bug when gas phase had no gas components. Looked the same as not having a gas phase at all. svn 1245: Enabled redox in Pitzer model with option in PITZER keyword. Typically, the option will be included in the pitzer database file. PITZER -redox TRUE The default database for the Pitzer model does not contain any redox definitions and the default value for the option is FALSE. At a minimum, species O2 and H2 must be defined in the database or input file to allow redox calculations. svn 1179: New option (-sites_units density) allows alternative units (sites/nm^2) for definition of number of sites for a surface. This approach requires better consistency among the parameters as both the number of sites and the surface area are based on the mass. It makes more sense than the default, which requires the number of sites (first numeric item in a line) to be defined in units of moles, independently of the number of grams of sorbent. SURFACE 1 -sites DENSITY SurfOH 2.6 600. 1.0 SurfaOH 2.6 30. 2.0 In this example, Surf has a site density of 2.6 sites per nanometer squared, a specific area of 600 meters squared per gram, and a mass of 1 gram. Surfa has a site density of 2.6 sites per nanometer squared, a specific area of 30 meters squared per gram, and mass of 2 grams. svn 1128: Fixed bug with value of time printed to selected output file when using cvode. Value printed was an intermediate integration time step, not time at end of integration. svn 1096: Allows solids and gases in the equations for PHASES. This capability simplifies the definitions for gas and solid isotopic components. Solids must be identified with "(s)" and gases with "(g)". The first entity on the left- hand-side of the equation must be the stoichiometric formula of the solid of gas component being defined, optionally with (g) or (s). In turn gases and solids included in the equation must be defined with reactions that ultimately allow the defined species (C[18O]2(g) in this case) in terms of aqueous species. C[18O]2(g) C[18O]2(g) + CO2(g) = 2CO[18O](g) log_k 0.602059991327962396 # log10(4) svn 1092: CD_MUSIC sorption model has been implemented. Still missing logic for surfaces related to equilibrium- phases and kinetics. Has explicit calculation of diffuse layer composition with Donnan assumption. Old diffuse-layer calculation will not be implemented. Example: SURFACE Goe_uniOH .000552 96.387 1 -capacitance 1.1 5 Goe_triO .000432 -cd_music -donnan 1.1 5 are capacitances for the cd-music model for 0-1 and 1-2 planes, respectively. -cd_music specifies that the surface is a cd-music surface. -donnan optionally calculates the diffuse layer composition with the Donnan model. SURFACE_SPECIES Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O log_k 20.1 # eq 7 K1, Kin1 -cd_music -1 -6 0 0.25 5 -cd_music gives the charge contribution of the surface species to the three planes. Plane 0 is -1 + 0.25*5; Plane 1 is -6 + (1-0.25)*5; Plane 2 (or d) is 0. svn 1030: Fixed bug in tranport. Mixing was not printed when using -cvode in kinetics. svn 984: Fixed bug in transport when cell without a surface followed a cell with a diffuse-layer surface. Fixed bug in TOTAL function; code ran of the end of the list of master species; changed logic to recognize the end of the list. svn 874: Fixed bug in check_same_model. Thought surface calculation was the same even though -edl switch was different, which gave irratic results and possible crash. Now checks more carefully to make sure calculation for surfaces is really the same and reinitializes if not. svn 847: Fixed bug with DESCRIPTION function. Did not give correct solution description for reactions. svn 826: Update tally.c to avoid conflicts in C++ version of phast. svn 801: Wrote around underflow in fabs in subroutine reset. svn 794: Errors in minteq.v4.dat database. Several redox reactions had delta H listed as kcal instead of kJ. kcal is correct only for the following species H2, NO2-, and NH4+. svn 675: Added PRINT option to print the species that contribute to alkalinity. Alkalinity distribution is printed in the output file following the distribution of species. Default at program startup is false. PRINT -alkalinity true svn 655: IAP and log K printed in Phase assemblage data block were calculated from reactions rewritten to new master species. Now the original data base reaction is used to calculate IAP and log K. Also fixed check that ensured all elements of phase in are in solution before SI is calculated. svn 631: Fixed bug with alternate formula for equilibrium phase, nothing happened if all other equations were satisfied at beginning of reaction calculation. svn 603: Link gmp library statically. svn 601: Fixed statement on multiprecision. svn 581: Fixed bug in PhreeqcI that did not reinitialize Chebyschev parameters leading to incorrect results with Pitzer activity coefficients. Results were correct on first run, but erroneous on subsequent runs. Added statement to identify multiprecision or standard solver for inverse modeling. svn 578: Distribution changes. Fixed names in README file. Modified Makefile to use specified version. Split Linux and source distribution procedure. ------------------------------------------------------------ Version 2.12 Date: Wed September 28, 2005 ------------------------------------------------------------ Executables and output files for Sun operating systems are no longer provided. Limited log activities of master species to be greater than the smallest machine precision exponential number. Avoids a matherr exception and allows trial of additional parameter sets to attempt to solve the system of equations. Made aqueous activity coefficients the default activity coefficients for exchange species when using the Pitzer formulation. New option in EXCHANGE is -pitzer_exchange_gammas T/F, default is true; defining "false" sets exchange activity coefficients to 1.0. Option has no effect for ion-association model (non-Pitzer). Edited phreeqc.dat to add -gamma expression for CdX2 and PbX2. Replaced O2(g) log K in phreeqc.dat and wateq4f.dat with data from llnl.dat, which appears to be better. Added multiplier format to REACTION increments, which simplifies definition of multiple equal reaction increments. REACTION H2O 1 -36 3*-4 2*-.25 -0.19 4*-0.1 3*-0.05 moles Added Pitzer activity formulation. Use pizer.dat database to invoke the Pitzer model. Should have same capabilities as ion-association model except explicit diffuse layer calculation is not implemented with the Pitzer model. Fixed bug in surface sites related to mineral and exchange sites related to mineral. Did not have complete logic to handle redox valence states in formula for species. Modified to remove non standard usage of va_list. Removed exchange master species from SYS("ex",..) list of species. This species is fictive and should not be included in the list. Changed -redox in SOLUTION so that if one of the redox states of a couple is not defined, then redox defaults to pe. Fixed buffer overrun in PhreeqcI with SOLUTION_SPREAD, caused segmenatation fault with lines greater than 500 characters. Added bigger string for some error messages to avoid access violation in cvode. Changed output_msg to warning_msg for combinations of convergence parameters so that message would be controlled by -warnings identifier. Carriage returns are now stripped from Basic program statements. Switching files from Windows to Unix sometimes leaves extra carriage returns at the ends of lines, which caused a syntax error for some Basic commands. Two bugs were fixed in inverse modeling. (1) Potential models are now checked for all equality and inequality constraints. Previously some constraints were not checked. (2) One loop of cl1 did not include the last row when checking for the pivot element. Also printing of headers was slightly modified for inverse modeling. A new multiple precision version of cl1 was develeped by using the Gnu Multiple Precision package (gmp). Calculations are carried out to about 30 significant digits. The mp version may help in some situations where roundoff errors are a problem, but it is still possible that roundoff errors will cause cl1mp to fail to find a solution to the optimization problem. The mp version has the following options in INVERSE_MODELING: -multiple_precision T/F--causes the mp version to be used in inverse modeling calculations. -mp_tolerance 1e-12--tolerance for mp version of cl1. As in cl1, numbers less than the tolerance are considered to be zero. 1e-12 is the default. -censor_mp 1e-20--as calculations occur in the linear equation array, elements less than this value are set to zero. Default is 1e-20. A value of 0.0 causes no censoring to occur. ------------------------------------------------------------ Version 2.11 Date: Mon February 7, 2005 ------------------------------------------------------------ Fixed error in selected output file with mixing reaction. MIX number was written to two columns, should be one. Fixed memory leak with PAD function. New database minteq.v4.dat has been translated from version 4.02 of MINTEQA2. An older version of the MINTEQA2 database is retained in file minteq.dat. Switched version control to subversion. Simplified, reorganized makefiles. Fixed bug with PRINT; -warnings n. Use of this option generally eliminated all warning messages instead of all messages after the nth. Default number of warning messages printed in now 100 per simulation. Fixed memory leaks in cvode that caused phreeqci to crash. Now uses PHRQ_malloc in case of other memory leaks. Also fixed potential memory error with PAD Basic function. Saturation index phases that included water had wrong value if distribution of species, exchange, or surface not written also. Fixed error message in cvode, if max iterations exceeded the error caused a segmentation fault. Made printing of parameter combination message a warning message so that it could be turned off. ------------------------------------------------------------ Version 2.10 Date: Tue November 2, 2004 ------------------------------------------------------------ Rearranged i/o for PHREEQC and reorganized driver subroutine. The object of these changes is to make the program more functional as a module for other programs (PHAST) and eventually to produce a callable C and Fortran module. Fixed a problem with surface related to a phase, when phase was not part of system (for example, Fe(OH)3a when there is no iron in system. Added convergence parameter set that requires mineral transfers to produce positive concentrations in the event that negative concentrations have been produced in the prior Newton-Raphson iteration. (Fluorite example). Fixed bug with kinetics formulas; did not account for stoichiometric coefficient correctly when using phase names. Generalized to allow multiple phase names in the -formula definition. ------------------------------------------------------------ Version 2.9 Date: Wed September 15, 2004 ------------------------------------------------------------ In inverse modeling, program terminates if sum of initial solutions and phases is > 32. Fixed bug with isotopes. Log activity estimate after initial solution calculation was inf under some conditions. An initial surface calculation failed when using D. Changed saturation index print out to use reaction and log K defined in PHASES definition. Previously, reaction could be rewritten to predominant redox species. Fixed incorrect print of elapsed time for kinetics in advection. Added phrqproto.h prototype file and phrqtype.h for switching compilation to long double. Fixed incorrect printout of kinetics delta moles with advection. Added convergence parameter set that skips mineral equations for first 5 iterations. Added entity_exists for module. Tried to fix bug with mix index incorrect (-2) for mixing with kinetics. Added new keyword COPY that allows a data entity to be copied from one index to a new index or to a range of indicies. Format is COPY keyword index index_start[-index_end] where keyword is one of the following: SOLUTION EQUILIBRIUM_PHASES EXCHANGE GAS_PHASE KINETICS MIX REACTION REACTION_TEMPERATURE SOLID_SOLUTION SURFACE Numerical method had a bug with ionic strength, if mass of water was not approximately 1. Routine revise_guesses did not divide by the mass of water. Also changed check in routine molalities to check by molality, not moles. Fixed a null pointer when surface was related to a mineral and mineral was not in database. Added new Basic functions i = INSTR(a$, b$) sets i to the character position of string b$ in a$, 0 in not found. b$ = LTRIM(a$) trims white space from beginning of string a$ and stores result in b$. b$ = RTRIM(a$) trims white space from end of string a$ and stores result in b$. b$ = LTRIM(a$) trims white space from beginning and end of string a$ and stores result in b$. Added new Basic function SYS that calculates the to total amount of an element in all phases (solution, equilibrium_phases, surfaces, exchangers, solid solutions, and gas phase). KINETIC reactions are not included. The function has two forms: (1) one element name as an argument (variable names are user specified) 10 t = SYS("As") the function will return the total arsenic in the system. (2) 5 argumens 10 t = SYS("As", count_species, names$, types$, moles) will return the total arsenic in the system to tot; count_species-- the number of species that contain arsenic, including solution, equilibrium_phases, surfaces, exchangers, solid solutions, and gas phase species; names$--a character array that has the name of each species; type$--a character array that specifies the type of phase for the species, aq, equi, surf, ex, s_s, gas, diff. Diff refers to the amount of the element in the diffuse layer of a surface when the explicit diffuse layer calculation is used; moles--an array containing the number of moles of the element in the species. The sum of moles(i) is equal to tot. SYS has several special arguments for the form SYS("arg", count, names$, types$, values) arg is one of the options listed below. count is a single numeric value and is the number of elements in the following arrays. name$ is an array of string values. type$ is an array of string values. values is an array of numeric values. Values of arg: elt_name returns total number of moles of element in system. count is the number of species for the element in the system, including aqueous, exchange, surface, equilibrium_phase, solid solution component, and gas phase "species". Arrays are filled for each "species"; values are moles. "elements" returns total number of moles of all elements, valence states, exchangers, and surfaces. count is number of elements, valence states, exchangers, and surfaces. Arrays are filled for each element, valence state, exchanger, and surface; values are moles. "phases" returns maximum saturation index of all phases. count is number of phases in system. Arrays are filled for each phase; values are saturation indexes. "aq" returns sum of moles of all aqueous species. count is number of aqueous species in system. Arrays are filled with each aqueous species; values are moles. "ex" returns sum of moles of all exchange species. count is number of exchange species in system. Arrays are filled with each exchange species; values are moles. "surf" returns sum of moles of all surface species. count is number of surface species in system. Arrays are filled with each surface species; values are moles. "s_s" returns sum of moles of all solid solution components. count is number of solid solution components in system. Arrays are filled with each solid solution component; values are moles. "gas" returns sum of moles of all gas components. count is number of gas components in system. Arrays are filled with each gas component; values are moles. Added new Basic function, DESCRIPTION, that has the value defined for the description field of the SOLUTION keyword line. Added alternative ordinary differential equation solver called CVODE, a set of C routines from the Lawrence Livermore National Labs. CVODE is part of the SUNDIALS package. CVODE is used in place of the Runge Kutta method when "-cvode true" is used within a KINETICS data block. KINETICS -cvode true Fixed error in SOLUTION_SPREAD, defining -redox did not set the default redox for the solutions that were defined; pe was always used as default. Modified code to allocate space differently for pp_assemblage, exchange, surface, gas_phase, kinetics, and s_s_assemblage. Enough space is allocated at beginning of distribute_initial_conditions. May speed up phast initialization and make better use of available memory. Changed gfw of water to 18 if isotopes of water are included. Solvent is [1H]2[16O]. Fixed a bug in surface integration where order of ions in the list of g's was incorrect. Pyrite rate was not 0 if supersaturated in phreeqc.dat and wateq4f.dat Segmentation error if a surface species was not defined with an equation that contained another surface species. In this case, the surface master species had been redefined to be an aqueous species (SOLUTION_SPECIES). ------------------------------------------------------------ Version 2.8 Date: Tue April 15, 2003 ------------------------------------------------------------ Updated arsenic data in wateq4f.dat to be consistent with Archer and Nordstrom (2002). Revised Basic interpreter to allow lines of any length and character strings of any length. Renumbering basic statement that included the function SURF in PhreeqcI caused SURF to be omitted and generated a syntax error. SURF and other functions had not been implemented in PhreeqcI. Fixed a bug in the Basic Interpreter. If elements of a dimensioned variable (character or number) were used on both sides of an equation, the result was erroneously stored in the last element of the variable used on the right-hand side instead of the element specified on the left-hand side. Using comma in some fields caused an infinite loop. Fixed bug with SOLUTION_SPREAD, Phreeqc was not calculating solution numbers for solution_spread solutions without solution numbers. Fixed bug with stagnant zone calculations. If solutions not defined for stagnant cells, PhreeqcI crashed. Added new state for calculations, PHAST. Previously phast used the state TRANSPORT, which caused some erroneous results with temperature when TRANSPORT was used in the PHREEQC part of the calculation. Trying to define dump file in TRANSPORT caused a file opening error. Fixed logic so now can open a file and the name can include blanks. ------------------------------------------------------------ Version 2.7 Date: Fri February 14, 2003 ------------------------------------------------------------ Initialized gfw in elements structure. Fixed bug where "time" would be wrong for initial solution calculation. Needed to initialize rate variables for PhreeqcI. Added print of simulation number to error file for phreeqci Limited printing of cell numbers to output file in advection calculations. Cell numbers only printed if results for cell are going to be printed. PhreeqcI captured status messages for kinetics, which made a very large error file in some cases and a long wait to view the output file in PhreeqcI. Now PhreeqcI does not capture these intermediate status messages. Removed old code related to redirecting error file Corrected error in transport where wrong time step was used for integration. Changes to speed up transport algorithm. Allow file names with spaces in selected_output file name and dump_file name. Modifications to work with RC1 phast log file. Allow any characters in square brackets for element name. - and + and perhaps others caused problems before. Fixed log molality of water in species printout, was equal to log activity of water. Also fixed basic function for LM. Changed solid solution prints to print 0 if solid solution is not present. Fixed bug if no rate name was defined before options in RATES. Fixed warning on Mac compilation in fpunchf. Fixed bug if isotopes were used but H and O isotopes were not defined. Fixed bug where special initial solution calculations were done at later calculation stages. Needed to set initial_solution_isotopes = FALSE; Fixed problem in C++ if structure name is same as member name. logk member of logk structure was renamed to log_k. Added identifier -add_constant to PHASES, EXCHANGE_SPECIES, SOLUTION_SPECIES, and SURFACE_SPECIES. -add_constant -0.301 log K is augmented by the specified constant. Added punch_isotopes and punch_calculate_values to allow printing isotope ratios and any CALCULATE_VALUES result. Added KEYWORDS: ISOTOPES Element -isotope isotope_name units standard_ratio -total_is_major T/F (OPTION IS DISABLED!!) CALCULATE_VALUES Name -start Basic statements, must have SAVE -end ISOTOPE_RATIOS (for printing) Name=Calculate_values_name Isotope_name ISOTOPE_ALPHAS (for printing) Name=Calculate_values_name Named_logk=named_expression_name Basic functions: calc_value("calc_value_name") evaluates a definition of CALCULATE_VALUES lk_named("name") log10(K) of definition in NAMED_EXPRESSIONS lk_phase("name") log10(K) of definition in PHASES lk_species("name") log10(K) of definition in (SOLUTION, EXCHANGE, SURFACE)_SPECIES sum_gas("template","element") Sum of element in gases with specified template template="{C,[13C],[14C]}{O,[18O]}2" includes all CO2 gases sum_species("template","element") Sum of element in aqueous, exchange, and surface species with specified template sum_s_s("s_s_name","element") Sum of element in a specified solid solution PRINT keyword: -initial_isotopes T/F -isotope_ratios T/F -isotope_alphas T/F -censor_species 1e-8 # Omits print of species if less than relative criterion SELECTED_OUTPUT keyword: -calculate_values name1 name2 ... -isotopes minor_isotope1 minor_isotope2 .... Added functions LK_SPECIES, LK_NAMED, LK_PHASE for Basic interpreter. LK_SPECIES("CaHCO3+") returns the log k for the association reaction for the ion pair CaHCO3+ at the current temperature. The log K is for the reaction as defined in the database or input file. Similarly, LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)") returns the value for the log K at the current temperature using expressions defined in NAMED_LOG_K data block; LK_PHASE("Calcite") returns the value of log K for calcite at the current temperature for the dissociation reaction defined in the database or input file. Values are "log10" values. Example for Basic program: 10 PRINT "Log10 KCalcite: ", LK_PHASE("Calcite") 20 PRINT "Log10 KCaHCO3+: ", LK_SPECIES("CaHCO3+") 30 PRINT " 1000ln(alpha): ", LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)")*LOG(10)*1000 Added NAMED_EXPRESSIONS data block. This data block was implemented to facilitate isotopic calculations. It allows analytical expressions that are functions of temperature to be defined. The purpose is to separate the fractionation factors from the log K, so that the fractionation factor or its temperature dependence can be easily modified. The named expression can be added to a log K for a species or phase by the -add_logk identifier in SOLUTION_SPECIES EXCHANGE_SPECIES, SURFACE_SPECIES, or PHASES data block. ------------------------------------------------------------ Version 2.6 Date: Mon April 22, 2002 ------------------------------------------------------------ PhreeqcI released. All selected_output is routed through a single routine. Allow "_" inside square brackets, [A_bcd]. Fixed bug match_elts_in_species, check for "e-" was wrong. Modified minteq.dat to put CuS4S5-3, Cu(S4)2-3 in in Cu(1) mole balance equations instead of Cu(2). Before the change, the program would not converge if Cu(2) were defined in an initial solution. Made revisions hopefully to improve SOLID_SOLUTIONS convergence with small numbers of moles of solids. Made changes related to dump file and PhreeqcI. Iterations now sums iterations in all kinetics calculations Fixed bug with LA("H2O"), which was returning natural log of activity of water. ------------------------------------------------------------ Version 2.5 Date: Mon October 1, 2001 ------------------------------------------------------------ In llnl.dat, fixed sign errors in RRE (rare earth elements) for some redox reactions and removed some redundant species, generally ReeO2- was retained and Ree(OH)4- was removed. Added the capability to use square brackets to define an "element" name. The brackets act like quotation marks in that any character string can be used within the brackets as an element name. This was introduced to simplify expansion of the model to isotopic species. [13C], [14C], and [18O] are legal element names. Added identifier -activity_water for a species in SOLUTION_SPECIES data block. This identifier has been added for future updates that will allow isotopic calculations. It is intended to be used only for isotopic variations of H2O, like D2O or H2[O18]. It forces the activity coefficient for the species to be activity(water)/55.5. This effectively sets the activity of the species to the mole fraction in solution. Fixed bug in checking solid solutions for presence or absence of elements in the system. Programming error caused segmentation fault if an error was detected under certain conditions. Changed return value of MOL to be molality of water if argument is "H2O". Also changed return value of LA to be activity of water if argument is "H2O". Diffuse layer calculation was incorrect if aqueous phase did not have 1 kilogram of water. Eq. 74 of manual has molality, but code used moles. The code was corrected by adding the mass of water to the formulation. Stagnant zones with first-order exchange approximation (1 stagnant cell, exchange factor, and porosities defined) did not work correctly if mobile and immobile cells did not have equal volumes of water. The mixing factors were revised to account for the masses of water in the stagnant and mobile zones. A fatal error was erroneously detected if the database file had a DATABASE data block. DATABASE data block is now ignored while reading the database file. Added identifier -bad_step_max to KINETICS data block. An integer following -bad_step_max gives the maximum number of times a rate integration may fail before execution of the program is terminated. Default is 500. ------------------------------------------------------------ Version 2.4.2: Date: Fri June 15, 2001 ------------------------------------------------------------ Fixed spreadsheet bug. Program was not ignoring columns that could not be identified as either element names or allowed data (ph, pe, number, description, etc). Also, the program failed if a spreadsheet solution number was negative. ------------------------------------------------------------ Version 2.4.1: Date: Mon June 4, 2001 ------------------------------------------------------------ Fixed spreadsheet bugs with isotopes. ------------------------------------------------------------ Version 2.4: Date: Fri June 1, 2001 ------------------------------------------------------------ Added structure for spreadsheet for use by PhreeqcI. Isotope value initialized incorrectly if only an -uncertainty was defined in SOLUTION_SPREAD. Fixed segmentation violation when primary and secondary master species were defined improperly. Corrected enthalpies of reaction in llnl.dat. Previous release had erroneously had enthalpies of formation in -delta_H parameter; the values should be enthalpies of reaction. Enthalpies of reaction were calculated from the enthalpies of formation and these values are now included in the -delta_H parameter. This change will have very little impact on calculations because the analytical expression has precedence over -delta_H in calculating temperature dependence of log K, and nearly all species and minerals have an analytical expression or lack both an analytical expression and an enthalpy of reaction. Corrected bugs in punch of solid solution components that caused both selected output and output file errors: moles were incorrect in selected output, and total moles and mole fraction were incorrect in output file. Added surface complexation constants for Fe+2; two complexes for weak sites and one complex for strong sites. phreeqc.dat and wateq4f.dat modified. Comment for units of parameters for calcite rate equation was wrong. Rate equation now uses cm^2/L for area parameter. Previously the correct units would have been 1/decimeter. phreeqc.dat and wateq4f.dat modified. Fixed a bug when rates were equal within tolerance, but negative concentrations occurred because of small initial concentrations. Added -warnings to PRINT keyword for specification of maximum number of warnings to print. Negative number allows all warnings to be printed. Function CELL_NO in Basic now prints a number equivalent to -solution in SELECTED_OUTPUT data block. This does not change printing for ADVECTION or TRANSPORT calculations. Kinetics time is halved for advective part of reaction in transport; time incorrectly accounted for before. -punch_ identifiers printed -1 instead of the correct solution number for batch-reaction calculations. -high_precision is no longer reset to false with every SELECTED_OUTPUT data block. SELECTED_OUTPUT file name stored for use by PhreeqcI. Alkalinity for NH3 corrected to 1.0 in llnl.dat. Fixed bug with USER_PRINT of kinetics. Did not find correct kinetics information in some cases. Fixed bug in default values for SOLUTION_SPREAD. Cannot use phase name and SI for pH or pe, and bug did not allow PHREEQC to run. Now PHREEQC runs, but warns that this is not allowed. ------------------------------------------------------------ Version 2.3: Date: Tue January 2, 2001 ------------------------------------------------------------ Added new keyword DATABASE. It must be the first keyword in the input file. The character string following the keyword is the pathname for the database file to be used in the calculation. The file that is specified takes precedence over any default database name, including environmental variable PHREEQC_DATABASE and command line arguments. Fixed bug in SOLUTION_SPREAD. If first heading in the spread-sheet input was an identifier--pH, pe, units, etc--then the headings were interpreted as an identifier and bad things happened. Added new keyword to make aqueous model similar to LLNL and Geochemists Workbench when using llnl.dat as the database file. Values of Debye-Huckel a and b and bdot (ionic strength coefficient) are read at fixed temperatures. Linear interpolation occurs between temperatures. New options for SOLUTION_SPECIES are -llnl_gamma a , where a is the ion-size parameter. -co2_llnl_gamma , indicates the temperature dependent function for the bdot term given in -co2_coefs of LLNL_AQUEOUS_MODEL_PARAMETERS will be used. Applies to uncharged species only. LLNL_AQUEOUS_MODEL_PARAMETERS -temperatures 0.0100 25.0000 60.0000 100.0000 150.0000 200.0000 250.0000 300.0000 #debye huckel a (adh) -dh_a 0.4939 0.5114 0.5465 0.5995 0.6855 0.7994 0.9593 1.2180 #debye huckel b (bdh) -dh_b 0.3253 0.3288 0.3346 0.3421 0.3525 0.3639 0.3766 0.3925 -bdot 0.0394 0.0410 0.0438 0.0460 0.0470 0.0470 0.0340 0.0000 #cco2 (coefficients for the Drummond (1981) polynomial) -co2_coefs -1.0312 0.0012806 255.9 0.4445 -0.001606 Fixed bug in basic interpreter. A number like "..524" would cause an infinite loop. Added function SURF to Basic. SURF("element", "surface") gives the amount of element sorbed on "surface". "surface" should be the surface name, not the surface-site name (that is, no underscore). Fixed option to "runge_kutta" from "runge-kutta" to match documentation for KINETICS. Fixed UO2+2 and Mn+2 reaction stoichiometry for Hfo surface complexation in wateq4f.dat. Added option for an equilibrium-phase to dissolve only. "dis" is added at the end of a line defining an equilibrium- phase. No data fields may be omitted. Should not be used when adding an alternative reaction. Example: EQUILIBRIUM_PHASES Dolomite 0.0 0.001 dis R-K integration failed when only the final rate generated negative concentrations. Allow decimals in definition of secondary master species, for example S(0.3). Fixed bug if description was more than about 85 characters; now allows about 400 characters. Fixed bug for surface/exchange sites related to phases. Was checking internal copies of surfaces/exchange with negative numbers. Fixed bug in quick prep that did not set the correct pointer for gas phases. Fixed segmentation fault that occurred if all elements for phase-boundary mineral were not in the solution. Only applied to a phase used to define concentration in an initial solution calculation. Added option to eliminate echo of input file in PRINT data block. -echo_input T/F turns echoing on and off. Default is on. ------------------------------------------------------------ Release 2.2: Date: Wed March 1, 2000 ------------------------------------------------------------ Fixed bug in MIX if no solutions are defined. Changed printout for surface. Only gives net surface charge for diffuse layer calculation. Prints correct value for the surface charge and surface charge density for diffuse-layer calculation. Added function EDL to Basic. EDL("element", "surface") gives the amount of element in the diffuse layer for "surface". not including sorbed species. "surface" should be the surface name, not the surface-site name (that is, no underscore). Special values for "element" include: "charge" - gives surface charge, equivalents. "sigma" - surface charge density, C/m**2. "psi" - potential at the surface, Volts. "water" - mass of water in the diffuse layer, kg. Changed distribution to be more consistent with other USGS water-resources applications. ------------------------------------------------------------ Release 2.1: Date: Wed January 19, 2000 ------------------------------------------------------------ Added additional #ifdef's for PhreeqcI. Fixed problem with formats for USER_PUNCH and others with Microsoft C++ 3 digit exponents. Initial Release 2.0: Date: Wed December 15, 1999 Version: C_54 = Version 2.0