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EnergyPlus has a warning when two vertices describing a surface are <0.01m (less than 0.4 inch) apart. This probably indicates two points that are intended to be the same. EnergyPlus assumes that the vertices were designed to be the same and drops one from the list of vertices for that surface. Extra vertices like this are often linked with other problems describing the building geometry. While it is a warning, it should not be ignored, and at minimum, the vertices shown in the error message should be examined to see if they were intended to describe the same point.