''in the light that the universe you claim is only matter and energy''
Do I?
Well that's news to me.
Based on the principles of physics - the inherit characteristics of matter/energy - matter/energy has evolved into highly complex structures, the most complex that we know of being the human brain.
The human brain, being an intelligent interactive system, is a powerful information processor that enables creative thinking and rearranging of information in an attempt to understand the world around it.
Part of that process, empathy, social needs, cohesion, safety, etc, drives the formulation of social rules and regulations and ethical standards, which relate to human needs. The things we need to keep us safe and allow some degree of fairness in society....the golden rule being an example.
“One should never do wrong in return, nor mistreat any man, no matter how
one has been mistreated by him.” - Socrates, dialogue with Crito. (Which is well before Christianity)
This drive to understand the world has also driven our supernatural explanations for how the world came about....but we now know that these are contradictory and not based on evidence.
You mention Stalin and Pol Pot as if they were motivated purely by atheism rather than the desire for personal power, which may also apply to theists such as Ivan the Terrible, except when those in religious orders are also motivated by religious imperatives to kill and torture for the glory of their God.
