Block mode is always good, but prefetch might be redundant. On Auto, all non-reserved IRQs get grabbed. The BIOS may try to be "smart" about when to enable the emulation. Legacy emulation is more likely to work right for the keyboard.
Just deletes everything FAST. This is the default if an unformatted harddisk is detected. The programs XMGR. SYS all come from a package called "the Jack R. Ellis drivers" or just "drivers. Since —, this collection of drivers has changed form many times without significant changes to function. The drivers have been revised, updated, deleted, re-added, merged, split, renamed, refactored, open-sourced, closed-sourced, plagiarized, and embargoed.
Most testing I did using the version, which remains in the Ibiblio archive under several different symlinks. The current incarnation, as of , is available from Johnson Lam's web site menu page , direct link.
Reasons to prefer the current version include, but are not limited to:. EXE if they exist. XHDD works around.
BAT as follows:. Unfortunately, it causes lockups with many sound cards and has other complications. I have not determined whether different versions of the driver make any difference. Accepted values for UIDE.
TXT, : 5, 15, 25, 40, 50, or any number from 80 to MiB. Accepted values for XHDD. TXT, : 5, 10, 15, or any number from 20 to MiB. This avoids lockups in some cases but not others. BAT it just hung every time. Its downside is that disk caching is essential to avoid a major slowdown.
W98 is a single-CPU operating system. Additional cores provide no benefit. If you want to operate on the sets as a whole, you should use the set operations popup from the Edit menu. You can sort according to any coordinate X, Y, DX, The set selector of the popup shows the number of points in each set in square brackets like this: G0.
S0[63], the points are numbered from 0 to n Using evaluate expression allows you to create a set by applying an explicit formula to another set, or to parts of another set if you use regions restrictions. All the classical mathematical functions are available cos, sin, but also lgamma, j1, erf, For the full list of available numerical functions and operators, see Operators and functions. In the formula, you can use X, Y, Y1, An implicit loop will be used around your formula so if you say:.
Beware that the loop is a simple loop over the indices, all the sets you use in such an hybrid expression should therefore have the same number of points and point i of one set should really be related to point i of the other set. If your sets do not follow these requirements, you should first homogenize them using interpolation. The histograms popup allows you to compute either standard or cumulative histograms from the Y coordinates of your data.
The bins can be either a linear mesh defined by its min, max, and length values, or a mesh formed by abscissas of another set in which case abscissas of the set must form a strictly monotonic array.
This popup is devoted to direct and inverse Fourier transforms actually, what is computed is a power spectrum. The default is to perform a direct transform on unfiltered data and to produce a set with the index as abscissa and magnitude as ordinate. You can filter the input data window through triangular, Hanning, Welch, Hamming, Blackman and Parzen filters. You can load magnitude, phase or coefficients and use either index, frequency or period as abscissas.
You can choose between direct and inverse Fourier transforms. If you specify real input data, X is assumed to be equally spaced and ignored; if you specify complex input data X is taken as the real part and Y as the imaginary part. If you want Grace can to use FFTW wisdom files, you should set several environment variables to name them.
The running average popup allows you to compute some values on a sliding window over your data. You choose both the value you need average, median, minimum, maximum, standard deviation and the length of the window and perform the operation.
You can restrict the operation to the points belonging to or outside of a region. The differences popup is used to compute approximations of the first derivative of a function with finite differences. The only choice apart from the source set of course is the type of differences to use: forward, backward or centered.
Beware that the period is entered in terms of index in the set and not in terms of abscissa! The integration popup is used to compute the integral of a set and optionally to load it. The numerical value of the integral is shown in the text field after computation. Selecting "cumulative sum" in the choice item will create and load a new set with the integral and compute the end value, selecting "sum only" will only compute the end value.
This popup is used to interpolate a set on an array of alternative X coordinates. This is mainly used before performing some complex operations between two sets with the evaluate expression popup.
The sampling array can be either a linear mesh defined by its min, max, and length values, or a mesh formed by abscissas of another set. Note that if the sampling mesh is not entirely within the source set X bounds, evaluation at the points beyond the bounds will be performed using interpolation parameters from the first or the last segment of the source set, which can be considered a primitive extrapolation.
This behaviour can be disabled by checking the "Strict" option on the popup. You can load either the fitted values, the residuals or the function itself.
Choosing to load fitted values or residuals leads to a set of the same length and abscissas as the initial set. Choosing to load the function is almost similar to load the fitted values except that you choose yourself the boundaries and the number of points. This can be used for example to draw the curve outside of the data sample range or to produce an evenly spaced set from an irregular one. The non linear fit popup can be used for functions outside of the simple regression methods scope.
With this popup you provide the expression yourself using a0, a1, You specify a tolerance, starting values and optional bounds and run several steps before loading the results. The fit characteristics number of parameters, formula, This popup can be used to compute autocorrelation of one set or cross correlation between two sets.
You only select the set or sets and specify the maximum lag. A check box allows one to evaluate covariance instead of correlation. You can use a set as a weight to filter another set. Only the Y part and the length of the weighting set are important, the X part is ignored. You can rotate, scale or translate sets using the geometric transformations popup.
You specify the characteristics of each transform and the application order. This popup provides two sampling methods. The first one is to choose a starting point and a step, the second one is to select only the points that satisfy a boolean expression you specify.
This popup is devoted to reducing huge sets and then saving both computation time and disk space. The interpolation method can be applied only to ordered sets: it is based on the assumption that if a real point and an interpolation based on neighboring points are closer than a specified threshold, then the point is redundant and can be eliminated. The geometric methods circle, ellipse, rectangle can be applied to any set, they test each point in turn and keep only those that are not in the neighborhood of previous points.
Given a set of curves in a graph, extract a feature from each curve and use the values of the feature to provide the Y values for a new curve. For single exponential curves, this is 2.
Read new sets of data in a graph. A graph selector is used to specify the graph where the data should go except when reading block data, which are copied to graphs later on. Reading as "Single set" means that if the source contains only one column of numeric data, one set will be created using the indices from 1 to the total number of points as abscissas and read values as ordinates and that if the source contains more than one column of data, the first two numeric columns will be used.
Reading as "NXY" means that the first numeric column will provide the abscissas and all remaining columns will provide the ordinates of several sets. Reading as "Block data" means all column will be read and stored and that another popup will allow to select the abscissas and ordinates at will. It should be noted that block data are stored as long as you do not override them by a new read.
You can still retrieve data from a block long after having closed all popups, using the set selector. The set type can be one of the predefined set presentation types see sets. The data source can be selected as "Disk" or "Pipe". In the first case the text in the "Selection" field is considered to be a file name it can be automatically set by the file selector at the top of the popup. In the latter case the text is considered to be a command which is executed and should produce the data on its standard output.
On systems that allows is, the command can be a complete sequence of programs glued together with pipes.
If the source contains date fields, they should be automatically detected. Several formats are recognized see appendix dates in grace. Calendar dates are converted to numerical dates upon reading. The "Autoscale on read" menu controls whether, upon reading in new sets, which axes of the graph should be autoscaled.
This entry exists only if Grace has been compiled with support for the NetCDF data format see configuration. Save data sets in a file. A set selector is used to specify the set to be saved. The plot appearance popup let you set the time stamp properties and the background color of the page.
The color is used outside of graphs and also on graphs were no specific background color is set. The time stamp is updated every time the project is modified. The graph appearance popup can be displayed from both the plot menu and by double-clicking on a legend, title, or subtitle of a graph see Clicks and double clicks. The graph selector at the top allows to choose the graph you want to operate on, it also allows certain common actions through its popup menu see graph selector.
Most of the actions can also be performed using the "Edit" menu available from the popup menubar. The main tab includes the properties you will need more often title for example , and other tabs are used to fine tune some less frequently used options fonts, sizes, colors, placements. If you need special characters or special formatting in your title or subtitle, you can use Grace escape sequences the sequence will appear verbatim in the text field but will be rendered on the graph , see typesetting.
If you don't remember the mapping between alphabetic characters and the glyph you need in some specific fonts mainly symbol and zapfdingbats , you can invoke the font tool from the text field by hitting CTRL-e. You can change fonts and select characters from there, they will be copied back in the text field when you press the "Accept" button. Beware of the position of the cursor as you enter text or change font in the font tool, the character or command will be inserted at this position, not at the end of the string!
You can save graph appearance parameters or retrieve settings previously saved via the "File" menu of this popup. In the "Save parameters" dialog, you can choose to save settings either for the current graph only or for all graphs. The set appearance popup can be displayed from both the plot menu and by double-clicking anywhere in a graph see Clicks and double clicks. The set selector at the top allows to choose the set you want to operate on, it also allows certain common actions through its popup menu see set selector.
The main tab gathers the properties you will need more often line and symbol properties or legend string for example , and other tabs are used to fine tune some less frequently used options drop lines, fill properties, annotated values and error bars properties for example. You should note that despite the legend string related to one set is entered in the set appearance popup, this is not sufficient to display it.
Displaying all legends is a graph level decision, so the toggle is in the main tab of the graph appearance popup. If you need special characters or special formatting in your legend, you can use Grace escape sequences the sequence will appear verbatim in the text field but will be rendered on the graph , see typesetting. The axis properties popup can be displayed from both the "Plot" menu and by double-clicking exactly on an axis see Clicks and double clicks.
The pulldown menu at the top allows to select the axis you want to operate on. The "Active" toggle globally activates or deactivates the axis all GUI elements are insensitive for deactivated axes. The start and stop fields depict the displayed range. Three types of scales are available: linear, logarithmic or reciprocal, and you can invert the axis which normally increases from left to right and from bottom to top.
The main tab includes the properties you will need more often axis label, tick spacing and format for example , and other tabs are used to fine tune some less frequently used options fonts, sizes, colors, placements, stagger, grid lines, special ticks, If you need special characters or special formatting in your label, you can use Grace escape sequences the sequence will appear verbatim in the text field but will be rendered on the graph , see typesetting.
Most of the controls in the dialog should be self-explanatory. One that is not and frequently missed is the "Axis transform" input field in the "Tick labels" tab. Entering there e. You can use any expression understood by the interpreter see command interpreter. Once you have set the options as you want, you can apply them. One useful feature is that you can set several axes at once with the bottom pulldown menu current axis, all axes current graph, current axis all graphs, all axes all graphs.
Beware that you always apply the properties of all tabs, not only the selected one. Set the properties of the display device. It is the same dialog as in Print setup. This menu item causes an update of all GUI controls. Usually, everything is updated automatically, unless one makes modifications by entering commands in the Command tool. Command driven version of the interface to Grace. The command will be parsed and executed, and the command line is placed in the history list.
Items in the history list can be recalled by simply clicking on them with the left mouse button. For a reference on the Grace command interpreter, see Command interpreter. The console window displays errors and results of some numerical operations, e. Suppose these curves represent the number of tasks a processor runs as the function of the number of users.
To make it more interesting, assume we are doing this in Quebec. Bring up the Axes pop up, select the Y axis, and click in the space to enter the label string of the axis label. Start typing Nombre de t. At this point we need to enter a accented letter, so we bring up the font tool by pressing Control-E.
You will now see what we have typed in the Cstring widget. Move the cursor to where you want to place the accented letter and click on the letter.
It should now appear in the string. You can either finish the string here or hit accept and keep editing. Label the x axis as well. This font tool is available wherever text needs to be entered. Our next exercise will be to title the graph so other. We can now fill in the title of the graph and by clicking on the "Titles" tab, the font and size and colour can be chosen.
The Viewport box under the "Main" tab defines the 4 corners of the graph frame. You can type them in or use the mouse to move them by first double clicking on them. Other things which can be controlled in this widget are the frame drawn around the graph, whether or not the graph background is coloured and the legends. Legends will be dealt with a little later.
Since we have several lines in our graph, it makes sense that we label them with a legend so that other people can figure out what they mean. The first thing to do is to give each set a label. This is done by entering a legend string for each set in the Set appearance popup. Now, from the Main form in the Graph appearance popup, click on "Display legend" to see the legend box. The location and appearance of the box is controlled by clicking on the "Leg. The appearance and spacing of the legend entries is controlled by the "Legends" tab.
For simplicity, label the sets alphabetically and then play with the appearance, etc. Specifying the placement of the graph by entering the coordinates can be painful, especially the fine tuning. To alleviate this problem, a graphical method is also available, although not readily apparent. After a legend appears, it may be dragged to a new location. To do this, press Ctrl-L with your mouse on the main canvas. You should see the arrow cursor turn into a hand.
If this doesn't work, double click on the main canvas to get its attention and then press Ctrl-L. Click on the legend and drag it. To cancel the legend drag mode as with all other modes , click on mouse button 3. I got bored so I took the data files and produced my own, albeit ugly, graph. See if you can copy mygraph. A block of data is a table of number which are interpreted as columns of numbers.
How sets are created from the columns depends on the information you want to extract from the file. We first need to read in a block of data. Select the file "3. If the read was successful, a window should pop up asking you to create a set from the block data. At the top it will list how many columns of data were read. Next we choose which column of data contains the x-ordinate. If there is no column, we can select "index" which will use the index into the column as the x ordinate starting from one.
If you close this window, it can reopened by bringing up a set list eg. Try creating a new set of type XYdY. This is an XY curve with error bars. Try X, Y, and Y1 the error from different columns.
Besides reading in data files, Grace has an extensive scripting language with a large number of math functions built in, These function include the basic add, multiply, square root, etc, and also the cephes library of higher order math functions like Bessel functions and the gamma function. Hence, functions in Grace are basically unlimited. See the user guide for more details. In addition, users can dynamically add libraries to Grace with any desired function. As well, points may be added manually to a set by the use of editors.
To create a set, press mouse button 3 the rightmost one for right handed people anywhere within the data set list which may be empty and select Create new. A menu with 4 different ways of creating new sets will be presented. We'll go through them one by one. Next, choose the type of set you would like to produce. This can be an extremely complicated function. Likewise, an expression for y is entered and for any other expressions that may be needed.
Fields after y are labelled y1, y2, y3 and y4. For example, if the set type xydxdy is chosen, y1 will hold dx and y2 will hold dy and it will be necessary to enter expressions for them. Pressing apply or accept will perform the calculations and create the new set. You may have to autoscale to see the new set. If your system has the Xbae widget set, this choice brings up a spreadsheet like editor to allow one to enter the points of the set by hand.
Initially, it just has the point 0, 0. Clicking on add will insert a copy of the currently selected row immediately below the selected row. Clicking delete will delete the row which contains the cursor. This method is best suited to examining or modifying existing sets or creating very small sets.
The sets gets updated after one hits enter or leaves the cell. If your system doesn't have the Xbae widget set or you want the power of your favourite external editor, a text editor of your choice may be used to enter data. If the set is new, it will contain only the point 0,0. During editing, no other operations are possible.
After the editor is closed, the set will be updated. Grace supports a large number of command line options which allow the user to control the appearance and placement of graphs.
This can be very useful if you want to use it to quickly print something without going through the GUI, use it within a script to automatically generate graphs, or have a plot come up already configured which can be much quicker than going through the GUI menus.
Invoking Grace with the command "grbatch"from the command line will cause Grace to start, produce a plot, send it to the printer unless a file is specified and then exit.
In its simplest form, to produce a plot of the file a. If gracebat is unavailable on your system, the hardcopy option to xmgrace will do the same thing. Assuming the hardcopy device is a postscript printer, one could also type.
Often, one wishes to plot several graphs with each graph having different characteristics. This is easily accomplished from the command line. Options specified on the command line are parsed in order and stay in effect until overridden by specifying them again. The first step in plotting multiple graphs is usually telling Grace how many graphs we have and how to arrange them.
The interpreter command "arrange" will do this. For example, if we want 4 graphs arranged in a simple 2x2 table, we specify -pexec "arrange 2, 2,. Specify any global options. Specify for each graph, the data to plot and any options. Options should be specified in the following order: "-graph g" where g is the graph number starting at 0.
This says to apply all following options to this graph. Set any autoscaling options. Remember, this setting is persistent. Set the set type. This is also a persistent setting. Specify the graph type and the input file. If reading in block data, create the sets with the "-bxy" option.
Specify any world scaling. It is important to do this AFTER sets are read unless autoscaling is off as the graph gets rescaled when data is read in. Specify anything else. Let's try an example. That said, under most conditions the adaptive integrator provides a much more efficient way of obtaining a fairly accurate result, as compared to the non-adaptive method.
If the solution is not sensitive to a change in adaptive. An additional indirect accuracy check is provided by the total charge conservation check echoed after each simulation see here. In this case the keyword currents should be followed by a list of variable names, with the number of variables in the list equal to the number of channels defined by the Ca.
Example 1: Run adaptive 1. As in the case of the adaptive simulation, each Run statement should be accompanied by a current definition statement, described above.
Example 1: Run 1. Example 2: Run 3. Different algorithms may be used for successive runs. Breaking up the simulation into multiple "runs" is desirable when the calcium channel currents change abruptly during the run, as when simulating channel opening and closing events.
If an adaptive method is used, it is important that the channel current is continuous during each of the individual "runs". This will limit the error arising from large current discontinuity. Thus, it is desirable to use Run adaptive 1. Here Time is the total integration time in ms , dt0 is the initial time step, and accuracy is the accuracy setting.
These values can be also set through assignment to the pre-defined constant names ODE. The type of output produced by plot instructions is controlled by the plot. To view the results in real time using the xmgr or the xmgrace programs, include the following command: plot.
Optional parameters "rows" and "cols" specify the arrangement of graphs within xmgr session window. Only simple point and 1D plot types will work in this regime; other plot types will be ignored. Note that there is a slight difference in viewport coordinates used by xmgrace vs xmgr. To correct for these differences, include one of the following two commands in the script file if you are using xmgrace : xmgrace. Data for each of the non-mute plots will be written to a file, if one includes the following command: plot.
This will work even in the plot. The format of the data files produced in this case is the same as the format used by the mute , 1D.
Below follows a list of implemented plot types. Syntax in the plot. One can also use the plot. The number of times each plot is refreshed is controlled by two parameters specifying respectively the resolution along the absicca time and ordinate concentration value axes; their names and default values are: plot.
To produce a data file instead of plotting, use plot 1D. The number of refresh plot update steps per simulation is set to by default; it may be changed by assigning a value to the parameter plot. If this number is equal to "1" , the concentration field values are only saved at the end of the simulation, as a two-column ASCII file, with the first column specifying the coordinate along the chosen axis, and the second number specifying the concentration value.
Note that for all 2D geometries , the argument coord2 should be omitted. For all 1D geometries , one should omit all three arguments axis , coord1 and coord2. This command will produce a 3-column ASCII file; in each row the first two numbers specify the 2D coordinate in the chosen plane, and the 3rd number is the value of the field at that point, at time T.
The file format is chosen for compatibility with the gnuplot plotting program, available for both Unix and Windows platforms.
Note that for all 2D geometries , the two arguments axis and coord should be omitted. The plot 2D. In this case, additional two real parameters can be specified they are optional , defining the angle and the fraction of z-scale devoted to function height, e.
The default number of saved time points per simulation is 40; this may be adjusted by assigning a different value to internal control parameter plot.
The binary data is written in the following sequence: 1 an integer specifying the geometry for Cartesian geometry, this is simply the number of dimensions ; 2 one to three integers specifying the number of nodes along each axis; 3 one to three double arrays specifying the coordinates of the axis nodes; 4 finally, for each time point, a time value double precision followed by the field concentration as a double precision array over all nodes.
To save the concentration fields at a single specified time point only, see dump plot below. This dump plot is particularly useful when combined with the import command to read it back into another simulation.
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