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The process of agent migration is the major difference between logical code mobility of software agents and physical mobility of mobile nodes in ad hoc networks. Without considering agent transfer, it would make little sense to mention the modeling of strong code mobility, which aims to make a migrated agent restarted exactly from the state when it was stopped before migration. From the perspective of system's architecture, this paper proposes a two-layer approach for the formal modeling of logical agent mobility (LAM) using predicate/transition (PrT) nets. We view a mobile agent system as a set of agent spaces and agents could migrate from one space to another. Each agent space is explicitly abstracted to be a component, consisting of an environmental part and an internal connector dynamically binding agents with their environment. We use a system net, agent nets, and a connector net to model the environment, agents, and the connector, respectively. In particular, agent nets are packed up as parts of tokens in system nets, so that agent transfer and location change are naturally captured by transition firing (token game) in Petri nets. Agent nets themselves are active only at specific places and disabled at all the other places in a system net. The semantics of such a two-layer LAM model is defined by transforming it into a PrT net. This facilitates the analysis of several properties about location, state, and connection. In addition, this paper also presents a case study of modeling and analyzing an information retrieval system with mobile agents.