The yammp module is written entirely in C and is presented to Python as a single large module. There is no entry point - main() - to this program; the closest thing to an entry point is the interface module - yammp.c. In the following, the links will open in a separate window. C Module Synopsis bounds.c Constrained dynamics contra.c CONTRA dynamics coords.c Manages the coordinates, gradients and velocities vectors. Also read and write archive files. dynam1.c Molecular Dynamics methods e_abhb.c Amber style hydrogen bond (10-12) term e_angl.c Angle term e_angn.c Generalized angle term e_bond.c Bond term e_elea.c Electrostatics term using an inclusion list e_iton.c Generalized improper torsion term e_itor.c Improper torsion term e_mors.c Bond term using the Morse potential e_nbna.c Volume exclusion term using an inclusion list e_nbnb.c Volume exclusion term using an exclusion list e_noen.c Generalized NOE bond term e_nonb.c Non bond terms using an exclusion list with electrostatics and Lennard-Jones e_nucl.c Experimental e_stud.c Stud binding term e_surf.c Surface term e_tors.c Torsion term e_vdwa.c Lennard-Jones term using an inclusion list e_vlat.c Vector Lattice term energy.c Entry point to the individual energy terms forces.c Dispatches calls to read sub-sections of the descriptor file mimesis.c service module minim1.c Energy minimization methods that use linesearch. minim2.c Other Energy minimization methods yammp.c interface module ycalc.c e_bond.c

The code can be organized into three layers: [1] Interface, [2] Methods and [3] Energies and Vectors. Only code in the outer layers call routines in the inner layers. In the following, the links will open in a separate window. Interface The yammp.c module collects all the methods modules and presents them to Python. The force field terms are read from the descriptor file in the forces.c module. yammp.c mimesis.c forces.c Methods The methods transform the coordinates and velocities vectors using the energies and gradient vectors calculated by the energy modules. monte.c minim1.c minim2.c dynam1.c bounds.c contra.c ycalc.c . Energies and Vectors Individual force field terms of energy and gradients are evaluated in the e_*.c modules. The individual terms are integrated in the energy.c module. The coordinates, velocities and gradient vectors are managed by the coords.c module. coords.c . . . . energy.c e_abhb.c e_angl.c e_angn.c e_bond.c e_elea.c e_iton.c e_itor.c e_mors.c e_nbna.c e_nbnb.c e_noen.c e_nonb.c e_nucl.c e_stud.c e_surf.c e_tors.c e_vdwa.c e_vlat.c