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Look in the 'Consolidation' section of the 'Interaction analyzes and advanced analyzes' chapter in the end of this manual on how to perform consolidation analyzes (combined groundwater flow with soil stress analyzes).
In case you have groundflow_total_pressure_atmospheric_cutoff set to -yes and the total pressure is 0, then Tochnog assumes that there is no water so the consolidation part in the equations will also be skipped. In case you have groundflow_total_pressure_atmospheric_cutoff set to -no this will not be done, so the consolidation part will also be used in case the total pressure is 0 (or positive).