Dot Clocks
        The standard VGA has two "standard" dot clock frequencies available to it, as well as a possible "external" clock source, which is implementation dependent.  The two standard clock frequencies are nominally 25 Mhz and 28 MHz.  Some chipsets use 25.000 MHz and 28.000 MHz, while others use slightly greater clock frequencies.  The IBM VGA chipset I have uses 25.1750 MHz  Mhz and 28.3220 crystals.  Some newer cards use the closest generated frequency produced by their clock chip.  In most circumstances the IBM VGA timings can be assumed as the monitor should allow an amount of variance; however, if you know the actual frequencies used you should use them in your timing calculations.
        The dot clock source in the VGA hardware is selected using the Clock Select field.  For the VGA, two of the values are undefined; some SVGA chipsets use the undefined values for clock frequencies used for 132 column mode and such.  The 25 MHz clock is designed for 320 and 640 pixel modes and the 28 MHz is designed for 360 and 720 pixel modes. The Dot Clock Rate field specifies whether to use the dot clock source directly or to divide it in half before using it as the actual dot clock rate.

Horizontal Timing
        The VGA measures horizontal timing periods in terms of character clocks, which can either be 8 or 9 dot clocks, as specified by the 9/8 Dot Mode field.  The 9 dot clock mode was included for monochrome emulation and 9-dot wide character modes, and can be used to provide 360 and 720 pixel wide modes that work on all standard VGA monitors, when combined with a 28 Mhz dot clock. The VGA uses a horizontal character counter which is incremented at each character, which the horizontal timing circuitry compares against the values of the horizontal timing fields to control the horizontal state. The horizontal periods that are controlled are the active display, overscan, blanking, and refresh periods.
        The start of the active display period coincides with the resetting of the horizontal character counter, thus is fixed at zero.  The value at which the horizontal character is reset is controlled by the Horizontal Total field. Note, however, that the value programmed into the Horizontal Total field is actually 5 less than the actual value due to timing concerns.
        The end of the active display period is controlled by the End Horizontal Display field.  When the horizontal character counter is equal to the value of this field, the sequencer begins outputting the color specified by the Overscan Palette Index field.  This continues until the active display begins at the beginning of the next scan line when the active display begins again.  Note that the horizontal blanking takes precedence over the sequencer and attribute controller.
        The horizontal blanking period begins when the character clock equals the value of the Start Horizontal Blanking field.  During the horizontal blanking period, the output voltages of the DAC signal the monitor to turn off the guns.   Under normal conditions, this prevents the overscan color from being displayed during the horizontal retrace period.  This period extends until the lower 6 bits of the End Horizontal Blanking field match the lower 6 bits of the horizontal character counter.  This allows for a blanking period from 1 to 64 character clocks, although some implementations may treat 64 as 0 character clocks in length.  The blanking period may occur anywhere in the scan line, active display or otherwise even though its meant to appear outside the active display period.  It takes precedence over all other VGA output.  There is also no requirement that blanking occur at all.  If the Start Horizontal Blanking field falls outside the maximum value of the character clock determined by the Horizontal Total field, then no blanking will occur at all.  Note that due to the setting of the Horizontal Total field, the first match for the End Horizontal Blanking field may be on the following scan line.
        Similar to the horizontal blanking period, the horizontal retrace period is specified by the Start Horizontal Retrace and End Horizontal Retrace fields. The horizontal retrace period begins when the character clock equals the value stored in the Start Horizontal Retrace field.  The horizontal retrace ends when the lower 5 bits of the character clock match the bit pattern stored in the End Horizontal Retrace field, allowing a retrace period from 1 to 32 clocks; however, a particular implementation may treat 32 clocks as zero clocks in length.  The operation of this is identical to that of the horizontal blanking mechanism with the exception of being a 5 bit comparison instead of 6, and affecting the horizontal retrace signal instead of the horizontal blanking.
        There are two horizontal timing fields that are described as being related to internal timings of the VGA, the Display Enable Skew and Horizontal Retrace Skew fields.  In the VGA they do seem to affect the timing, but also do not seem to be necessary for the operation of the VGA and are pretty much unused.  These registers were required by the IBM VGA implementations, so I'm assuming this was added in the early stages of the VGA design for EGA compatibility, but the internal timings were changed to more friendly ones making the use of these fields unnecessary.  It seems to be totally safe to set these fields to 0 and ignore them.  See the register descriptions for more details, if you have to deal with software that programs them.

Vertical Timing
        The VGA maintains a scanline counter which is used to measure vertical timing periods.  This counter begins at zero which coincides with the first scan line of the active display.  This counter is set to zero before the beginning of the first scanline of the active display.  Depending on the setting of the Divide Scan Line Clock by 2 field, this counter is incremented either every scanline, or every second scanline.  The vertical scanline counter is incremented before the beginning of each horizontal scan line, as all of the VGA's vertical timing values are measured at the beginning of the scan line, after the counter has ben set/incremented.  The maximum value of the scanline counter is specified by the Vertical Total field.  Note that, like the rest of the vertical timing values that "overflow" an 8-bit register, the most significant bits are located in the Overflow Register.  The Vertical Total field is programmed with the value of the scanline counter at the beginning of the last scanline.
        The vertical active display period begins when the scanline counter is at zero, and extends up to the value specified by the Vertical Display End field.  This field is set with the value of the scanline counter at the beginning of the first inactive scanline, telling the video hardware when to stop outputting scanlines of sequenced pixel data and outputs the attribute specified by the Overscan Palette Index field in the horizontal active display period of those scanlines.  This continues until the start of the next frame when the active display begins again.
        The Start Vertical Blanking and End Vertical Blanking fields control the vertical blanking interval.  The Start Vertical Blanking field is programmed with the value of the scanline counter at the beginning of the scanline to begin blanking at.  The value of the End Vertical Blanking field is set to the lower eight bits of the scanline counter at the beginning of the scanline after the last scanline of vertical blanking.
        The Vertical Retrace Start and Vertical Retrace End fields determine the length of the vertical retrace interval.  The Vertical Retrace Start field contains the value of the scanline counter at the beginning of the first scanline where the vertical retrace signal is asserted.  The Vertical Retrace End field is programmed with the value of the lower four bits of the scanline counter at the beginning of the scanline after the last scanline where the vertical retrace signal is asserted.

Monitoring Timing
        There are certain operations that should be performed during certain periods of the display cycle to minimize visual artifacts, such as attribute and DAC writes.  There are two bit fields that return the current state of the VGA, the Display Disabled and Vertical Retrace fields. The Display Disabled field is set to 1 when the display enable signal is not asserted, providing the programmer with a means to determine if the video hardware is currently refreshing the active display or it is currently outputting blanking.
        The Vertical Retrace field signals whether or not the VGA is in a vertical retrace period.  This is useful for determining the end of a display period, which can be used by applications that need to update the display every period such as when doing animation.  Under normal conditions, when the blanking signal is asserted during the entire vertical retrace, this can also be used to detect this period of blanking, such that a large amount of register accesses can be performed, such as reloading the complete set of DAC entries.

Miscellaneous
        There are a few registers that affect display generation, but don't fit neatly into the horizontal or vertical timing categories.  The first is the Sync Enable field which controls whether the horizontal and vertical sync signals are sent to the display or masked off.  The sync signals should be disabled while setting up a new mode to ensure that an improper signal that could damage the display is not being output.  Keeping the sync disabled for a period of one or more frames helps the display determine that a mode change has occurred as well.
    The Memory Refresh Bandwidth field is used by the original IBM VGA hardware and some compatible VGA/SVGA chipsets to control how often the display memory is refreshed.  This field controls whether the VGA hardware provides 3 or 5 memory refresh cycles per scanline.  At or above VGA horizontal refresh rates, this field should be programmed for 3 memory refresh cycles per scanline.  Below this rate, for compatibility's sake the 5 memory refresh cycles per scanline setting might be safer, see the Memory Refresh Bandwidth field for (slightly) more information.

 
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