FileVMDPatch

class FileVMDPatch : public feasst::FileVMD

Print a vmd script to view an xyz file via command “vmd -e file.vmd”

Make a patch by inscribing sphere of radius r2 inside bead of radius r1=sig. The distance between center of sphere and bead is given by “d.” For given patch angle, use law of cosines to derive r2 via constraint r1 + eps = r2 + d, where eps is small, to avoid clipping.

class PrinterXYZPatch : public feasst::LoopConfigOneBody

class FileXYZPatch

Similar to FileXYZ, except for patches.

Public Functions

void load(const std::string file_name, Configuration *config) const

Load the xyz file with file_name into the configuration. Note that this function does not read the domain tilts xy, xz and yz. This function also does not read the site types. Thus, particles should be added to the system in the desired order. If no particles in the configuration, use the first particle type.

void write(const std::string file_name, const Configuration &config, const int num_decimal_places = 8) const

Write the configuration to file_name in xyz format. If the simulation is 2D, simply writes z as 0.

param num_decimal_places:

Number of decimal places

Arguments

• group_index: print the coordinates of this group index only (default: 0).

• append: append file output if set to true. Do not append if false (default: “false”).