Atoms are the smallest units of matter which are independent and have a definite address. Atoms of different elements are different in many aspects but size and atomic weight are the main attributes. I think there is no such thing as color of things.
Color exists only when there is light. When the darkness falls, the color of things begins to dissolve and black color takes over everything. Black color thus obliterate all the differences due to colors.
May be this is the reason why in Hindu mythology many Gods are dark complexioned. Take for example Rama, Krishna and Draupadi, all of them are dark in complexion. Although it is strange to explain why so many of Hindus prefer the fair color.
So how can a thing have red color and black color at two instances of time? Light a bulb and again colors come back but there is different between the colors of things in different kinds of lights.
Sunlight is a mixture of many colors which are different waves. All the waves are the part of what is called light spectrum. Our eyes can see limited spectrum of light called visible spectrum which is from violet to red.
Violet and beyond region called ultra violet have higher energy. On the opposite end is the red color and lower energy infra red. Birds and bees are endowed with more complex eyes and are capable of seeing into the infrared and ultra violet ranges also. The plants have exploited this capability and deposit substances on the flower strategically on flowers so that bees reach the target directly.
Our eyes have light receptors called cones and rods. They gather light from the target and send to the brain for generating a composite picture. The rods are more numerous than cones.
The rods are meant for collecting the faint lights and operate when the light is dim like the sailors panning the stars in sky or when we are out in remote village on a clear night. Due to the plenty of light during the nights also these days, the services of the rods are seldom impressed upon. Now the main role is played by the cones. It is not known why these rods have not been traded with cones during the evolution.
When the light falls upon a substance, different energy centers in the substance become excited. These centers are electrons, atoms or molecules rotation, vibration of atoms joined with different kinds of bonds like single, double or triple.
Depending upon the available spectrum of rays falling on the substance, those matching these centers are absorbed. This match is very much defined depending on the structure of the molecules.
From the visible spectrum, some of the wave length rays are absorbed. Those which does not match any center is not absorbed and reflected back. This is the color which reaches our eye and is responsible for the color which we attribute to the substance.
Most of the optical analytical instruments use monochromatic light beams to shine on the atoms and molecules. Monochromatic light is pure light beam of single energy and generally matches a particular wavelength emitted by an excited atoms of single elements. Thus they are able to determine the concentration of a particular element in a solution.