Data format =========== .. _xml-format: XML format ---------- We take XML format files as the standard input and output configuration files. The XML files can contain coordinates, types, masses, velocities, bond connections, angles, dihedrals and so on. Here is an example of the XML file of a single molecule system. The molecule consisting of four particles is depicted in following picture. .. image:: xml-config.png :width: 250 px :align: center :alt: Principle of dihedral torsion The data in a line of XML file corresponds to a particle and all particles are given in sequence. For example, the coordinate of a particle in x, y, and z directions is written in a line and three columns in XML files. However, this rule does not include topological relevant information, including bonds, angles and dihedrals. An example XML file with particles coordinates, velocities, types, masses ... :: -1 2 -1 -2 3 0 -1 4 1 -1 5 2 1 2 3 1 0 0 3 -2 1 0 1 1 A B B A 1.0 2.1 1.0 1.0 The file could include the nodes of bond, angle, dihedral ... :: # bond with 'bond type, the index of particle i, j'. polymer 0 1 polymer 1 2 polymer 2 3 # angle with 'angle type, the index of particle i, j, k'. theta 0 1 2 theta 1 2 3 # dihedral with 'dihedral type, the index of particle i, j, k, l'. phi 0 1 2 3 The other nodes of XML ... :: # the diameter of particles in float type. 1.0 1.0 1.0 1.0 # the charge of particles in float type. 1.333 1.333 -1.333 -1.333 # the body index of particles in int type, -1 for non-body particles. -1 -1 0 0 # the image in x, y, and z directions of particles in int3 type, # which can be used for the calculation of pos0 with pos0 = pos + L*image, # where pos is the position in box, pos0 is the position without periodic boundary condition, # and L is the length of box. 0 0 0 0 0 0 0 0 0 0 0 0 # the velocity in x, y, and z directions of particles in float3 type. 3.768 -2.595 -1.874 -3.988 -1.148 2.800 1.570 1.015 -3.167 2.441 -1.859 -1.039 # the orientation vector (x, y, z) of particles in float3 type. -0.922 0.085 0.376 -0.411 -0.637 -0.651 0.293 0.892 -0.342 -0.223 0.084 0.970 # the quaternion vector (x, y, z, w) of particles in float4 type. 0.369 0.817 -0.143 0.418 -0.516 -0.552 0.653 0.024 -0.521 -0.002 0.131 0.843 -0.640 0.159 -0.048 -0.749 # the angular velocity of rotation in x, y, and z directions of particles in float3 type. -0.640 0.571 -0.512 -0.744 0.346 0.569 0.620 -0.086 0.779 -0.542 0.319 -0.776 # the moment of inertia in x, y, and z directions of particles in float3 type. 1.0 1.0 3.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 1.0 3.0 # the initiator indication of particles in int type, 1 for initiator. 0 1 0 1 # the crosslinking number of particles in int type, 0 for reactable monomer. 0 0 0 0 # the molecule index of particles in int type. 0 0 1 1 The nodes of anisotropic particle attribute ... :: # the particle patch attribute with 'particle type, patch number' # followd by 'patch type, patch size, patch position vector in x, y, z directions'. B 2 p1 60 0 0 1 p1 60 0 0 -1 # the patch-patch interaction parameter with 'patch type, patch type, gamma_epsilon, alpha'. p1 p1 88.0 0.5 # the particle shape attribute with 'particle type, diameter a, diameter b, diameter c, # epsion a, epsion b, epsion c'. The a, b, c are along x, y, z directions in body frame, # respectively. A 1.0 1.0 1.0 3.0 3.0 3.0 B 1.0 1.0 3.0 1.0 1.0 0.2