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Letsencrypt on virtualmin will require a domain name as it writes a files to that domain and if it cannot do so will throw up an error and the cert will not be granted.
Open up an SSL client.
You can install letsencrypt separately .. on ubuntu its sudo apt-get install letsencrypt.
Stop apache so port 80 is free.
Then in the command line type sudo letsencrypt certonly --standalone --agree-tos --email name@domain.tld -d domain.tld -d www.domain.tld
change domain to the domain you want the cert for and also the name in the email part.
Letsencrypt will create the cert. If it doesn't then I suspect there is an issue with your server. You will find the cert in etc/letsencrypt/live
Start apache