pHCalc performs several tasks after the titration of an acid using
a base as the titrant has been finished. It calculates the equivalence
point together with its pH value based on the second derivative. After
having performed the calculation, it prints the results into a neatly
formatted table and stores it in a file.
Additionally, it plots a titration curve
together with the first and second derivatives. To accomplish it, it
needs the values of the added titrant in mL and the measured pH
values during the addition of the titrant.
JDK:
- 11 or above. Both the Java compiler and Java runtime (JRE) need to support 64-bit. Compatible Java compilers as well as JREs can be downloaded from Bellsoft.
Memory:
- No minimum requirement.
Disk:
- Approximately 450 KiB is required for the compilation of pHCalc itself. In addition to that, 56 MiB disk space will be used for pHCalc.
Operating System:
- Windows: Windows 2000 or above.
- Unix based systems (Linux, Solaris and Mac OS X) and others: No minimum requirement.
Gnuplot:
- pHCalc uses gnuplot to plot the diagram. So you need to install gnuplot first before using pHCalc.
If you decide to compile this project then you can do it with maven. Under Linux open a terminal and go to the directory of this project. Then run the following command which will compile the source files:
$ mvn clean installAfter a successful compilation the .jar containing all the libraries
will be placed in the subfolder called target.
If you want to use the provided binaries, i.e. the release package
instead, then the installation process is simple. Please note, there
are two different binaries, one java binary that you can run like a
script in your terminal and another one which you run just like any
other jar file.
- Unpack the archive where you would like to store the binaries, e.g.:
$ tar -xvzf pHCalc-x.y.zip
- A directory called myPHCalc will be created.
-
Unix-based operating systems (Linux, Solaris and Mac OS X)
$ java -jar pHCalc-x.y.jar -h
-
Windows Open the windows command prompt or the powershell and enter the following command to display the help message:
$ java -jar pHCalc-x.y.jar -h
-
Alternatively, use the script like java file:
$ ./pHCalc -h
-
To perform some calculations, print its results and create a diagram you'll need a data file with two columns in the following order:
Volume of Titrant in mL (=X),pH (=Y)see example file -
The pHCalc's jar or script file as well as the settings file phcalc.properties need to share the same directory.
-
Additionally, you'll need to edit the settings file
phcalc.properties. Especially, the paths to the data file and to the new diagram file have to be entered. Without a correct path to the data file, pHCalc won't work.
log.size=<Number>
Define the size of the log that will be printed after pHCalc has finished a task.
language=(en | de)
possible values:
defor German,enfor English
mol.mass.acid=<Number: g/mole>
Enter the molar mass of the acid used in grams per mole.
sample=<Number: mL>
Enter the volume of sample that has been used for the titration.
dilution=<Number | 0 |: mL>
If the sample of the acid used has been diluted then you enter the (amount of water + sample size of the acid)
solution=<Number | 0 |: mL>
If the acid has been diluted and the titration has been performed using a specific amount of the diluted acid then you'll enter the amount of the final solution here. For example, original sample of the acid is 50 mL. Then you dilute this sample until the flask reaches 100 mL. From this diluted amount you take a 20 mL solution. Then you enter 20.
acid.formula=<Formula of the acid: Text>
acid.name=<Name of the acid: Text>
mol.mass.titrant=<Number: g/mole>
Enter the molar mass of the base, i.e. titrant used in grams per mole.
titrant.formula=<Formula of the base: Text>
titrant.name=<Name of the base: Text>
threshold=<Number>
Specify the difference between two pH values where you think the equivalence point has been reached. A good difference is for example, 1.5 or 2.5. It depends on your data rows.
sample.name=<Name of the sample: Text>
Enter the sample name that should appear in the results table or displayed on the chart.
chart.title=<Title of the chart: Text>
y.label=<Label of the y axis: Text>
x.label=<Label of the x axis: Text>
data.file=<Path/to/data.dat>
chart.file=<Path/to/chart.eps>
The chart will be created as a .eps file.
xtic=<Number: xtics>
ytic=<Number: ytics>
xtic.rotate=<Number: Rotation of the xtics labels in degrees>
param.b=<Number | 0>
Growth rate. For a standard logistic curve this is 1 so 1 is a reasonable estimate
param.n=<Number | 0>
Parameter that affects near which asymptote maximum growth occurs. 1.0 if we assume the curve is symmetric
param.q=<Number | 0>
Parameter that affects the position of the curve along the ordinate axis.
step=<Number | 1>
Specify of how many x values the fitted curve should consist of. Enter 1 if the fitted curve should contain as many x values as the data file.
The subcommands, its options and parameters apply to both the jar file and the script file. Please note that * stands for required option.
- Print the help message and the available subcommands
$ ./pHCalc [-hVv] [--] (compute | print | plot)| Option | Argument | Long Option | Option Description |
|---|---|---|---|
| -v | --[no-]verbose | Specify multiple -v options to increase verbosity: -v -v -v -v or -vvvv |
|
| -V | --version | show version number | |
| -h | --help | Show this help message |
- For example: Display the help menu for the subcommand plot
$ ./pHCalc help plot- For example: Display the general help message
$ ./pHCalc -h- Calculate the equivalence point as well as its pH value
$ ./pHCalc [OPTION] compute [<FILE>]| Option | Argument | Long Option | Option Description |
|---|---|---|---|
| -v | --[no-]verbose | Specify multiple -v options to increase verbosity: -v -v -v -v or -vvvv |
|
| -V | --version | Show version number | |
| -h | --help | Show this help message | |
| FILE | Save the table in a file # optional |
- For example:
$ ./pHCalc compute -v file1.txt- Print the calculations in a neatly formatted table
$ ./pHCalc [OPTION] print [-t=<TYPE>] [<FILE>]| Option | Argument | Long Option | Option Description |
|---|---|---|---|
| -v | --[no-]verbose | Specify multiple -v options to increase verbosity: -v -v -v -v or -vvvv |
|
| -V | --version | show version number | |
| -h | --help | Show this help message | |
| * -t | TYPE | --type | Type of table: all, results, data |
| FILE | Saves the table in a file # optional |
- For example: Print the data rows together with the first and second derivatives in one table and save it in a file:
$ ./pHCalc print -v -t=data data.txt- Plot the calculations or the data rows.
$ ./pHCalc [OPTION] plot [-fsyx] [-t=<TYPE>] [-a=<ASYMPTOTE>] [--color-curve=<COLOR>] [--color-ep=<COLOR>] [--color-firstDerivative=<COLOR>] [--color-secondDerivative=<COLOR>]| Option | Argument | Long Option | Option Description |
|---|---|---|---|
| -v | --[no-]verbose | Specify multiple -v options to increase verbosity: -v -v -v -v or -vvvv |
|
| -V | --version | show version number | |
| -h | --help | Show this help message | |
| -lc | --list-colors | Display available colors | |
| * -t | TYPE | --type | Type of plot: curve, derivatives, all |
| -f | --[no-]fit | Fit the titration curve # optional | |
| -s | --[no-]smooth | Smooth the curve(s) # optional | |
| -x | --[no-]xtics | Insert xtics # optional | |
| -y | --[no-]ytics | Insert ytics # optional | |
| -a | ASYMPTOTE | --asymptote | Set the parameters n and b used for curve fitting # optional |
| -c | COLOR | --color-curve | Color of the titration curve # optional |
| -cep | COLOR | --color-ep | Color of the equivalence point # optional |
| -c1 | COLOR | --color-firstDerivative | Color of the first derivative # optional |
| -c2 | COLOR | --color-secondDerivative | Color of the second derivative # optional |
- For example: Display all the available colors used for plotting the curves:
$ ./pHCalc plot --list-colors- For example: Plot only the titration curve using logistic regression to fit the curve:
$ ./pHCalc plot -a=STEEP_CURVE -t=curve -c=DARK_RED -fsy -vv- For example: Plot the titration curve including the derivatives by fitting the titration curve and smoothing all the curves:
$ ./pHCalc plot -a=STEEP_CURVE -c=DARK_MAGENTA -c1=FOREST_GREEN -c2=ORANGE_RED -fsx -t=derivatives -vv - For example: Plot the titration curve including the derivatives and the equivalence point by fitting the titration curve and smoothing all the curves:
$ ./pHCalc plot -a=STEEP_CURVE -c=DARK_RED -c1=FOREST_GREEN -c2=ORANGE_RED -cep=NAVY -fsx -t=all -vv If fitting is applied then pHCalc will use logistic regression to fit
the titration curve. However, to fit the titration curve successfully the
parameters n and b need to be suitable for a specific curve. These
parameters need to be set if option -f is applied. But there are
arguments of the asymptote which contain predefined values or which
have phCalc find suitable values:
SYMMETRIC_CURVE: Use this asymptote if the curve looks somehow symmetric. An example of it can be found here.
FLAT_CURVE: Use this asymptote if the titration curve is quite flat as in the titration of the phosphoric acid.
STEEP_CURVE: Use this asymptote if the curve is rather steep.
ADVANCED_CALC: Use this asymptote if parameters n and b should
be calculated by pHCalc.
SIMPLE_CALC: The same as the advanced_calc argument but the
calculation method is simpler.
NONE: Use this asymptote if you want to set the parameters n and
b by yourself in the settings file phcalc.properties.
Please note, the predefined values as well as the calculated ones
don't guarantee that the logistic regression will accept these values.
pHCalc will catch the exception and you'll notice it if you turn on
the third level of verbosity -vvv. In thoses cases you need to enter
the values for the paramters n and b manually in phcalc.properties
while on the command line you need to specify -a=NONE as the argument.
It's not necessary to enter a file name for displaying the calculations in neatly formatted tables. Without entering a file, you can view the table in your terminal.
pHCalc(R) Version 1.0 19/01/2023