I thank SAP2000 will be able to analysis your model if you want send me the model you want to do or tell me what you want and I will tray to help you

Yours

FOXTA is a program for the design of shallow foundations, deep foundations, pile groups, piled-raft foundations, rigid inclusions, etc

demo version can be downloaded from their website

APRAF, using a combination of finite layer and finite element methods to model layered soil, raft and piles, can be used to calculate the displacements, bending moments and shear forces in rafts and piles.

GEOTEC Office is a package of programs for geotechnical and design engineering. The package contains the following programs and tools: ELPLA: Analyzing footings, rafts, piled rafts, pile groups and foundation groups

The free version of geotec office can be downloaded from their website. 

you can search more programs on this website for piled raft system here. http://www.geotechnicaldirectory.com/page/software/Piles_(lateral_loading_and_groups)_.html

http://geotecoffice.com/

Dear Umer,

It's seen that all of these software are commercial package. I need an open source one, to change it.

best regard,

Dear Ouassim,

Thanks for response. Do you Install and use of FREEFEM? There is many file in its directory. Can you help me?

Try GeoStudio

opensees could be a good alternate for your purpose. you can add your element or material in its liberary . but , you had to better know it isn't easy and requires so much efforts. 

Opensees is a good open source software to model soil.

In this website you can find side by side comparison chart of 78 Finite Element Analysis (FEA) programs and their sorting by features:

http://feacompare.com/sortbyfeatures.html

https://www.researchgate.net/project/ADONIS-A-Free-Nonlinear-Finite-Element-Program-for-Geo-Engineers

I am agree with Reza Amini