This paper describes 3D simulations of the formation of collapsing cold clumps via thermal instability inside a larger cloud complex. The initial condition was a diffuse atomic, stationary, thermally unstable, 200pc diameter spherical cloud in pressure equilibrium with low density surroundings. This was seeded with 10% density perturbations at the finest initial grid level (0.29pc) around n_H = 1.1cm^{-3} and evolved with self-gravity included. No magnetic field was imposed. Resimulations at a higher resolution of a region extracted from this simulation (down to 0.039pc), show that the thermal instability forms sheets, then filaments and finally clumps. The width of the filaments increases over time, in one particular case from 0.26 to 0.56pc. Thereafter clumps with sizes of around 5pc grow at the intersections of filaments. 21 distinct clumps, with properties similar to those observed in molecular clouds, are found by using the FellWalker algorithm to find minima in the gravitational potential. Not all of these are gravitationally bound, but the convergent nature of the flow and increasing central density suggest they are likely to form stars. Further simulation of the most massive clump shows the gravitational collapse to a density >10^6 cm^{-3}. These results provide realistic initial conditions that can be used to study feedback in individual clumps, interacting clumps and the entire molecular cloud complex.
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