Data output =========== Common functions for Data output -------------------------------- .. py:function:: setPrecision(int npre) Set the number of places after decimal point. .. py:function:: setHead(int nhead) Set the number of places before decimal point. Collective information ---------------------- .. py:class:: DumpInfo(all_info, comp_info, filename) Constructor of an information dump object for a group of particles. :param AllInfo all_info: System information. :param ComputeInfo comp_info: Object for calculating collective information. :param str filename: Output file name. .. py:function:: dumpAnisotropy() Outputs information related to anisotropic particles. .. py:function:: dumpVirial(Force object) Outputs virials of the Force object. .. py:function:: dumpPotential(Force object) Outputs potentials of the Force object. .. py:function:: dumpVirialMatrix(Force object) Outputs virial matrixes including 'virial_xx', 'virial_xy', 'virial_xz', 'virial_yy', 'virial_yz', and 'virial_zz' of the Force object. .. py:function:: dumpPressTensor() Outputs press tensors including 'press_xx', 'press_xy', 'press_xz', 'press_yy', 'press_yz', and 'press_zz' of the system. .. py:function:: dumpTypeTemp(string type) Outputs temperatures of a type of particles. .. py:function:: dumpParticleForce(int tag_i) Outputs the forces of a particle indicated by tag_i in order to trace it's force condition. .. py:function:: dumpParticlePosition(int tag_i) Outputs the positions of a particle indicated by tag_i in order to trace it's position. .. py:function:: dumpBoxSize() Outputs box sizes including the box lengths in 'X', 'Y', and 'Z' directions and volume. .. py:function:: setPeriod(int period) Period to output data. Example:: dinfo = gala.DumpInfo(all_info, comp_info, 'data.log') dinfo.setPeriod(200) app.add(dinfo) MOL2 dump --------- .. py:class:: MOL2Dump(all_info, filename) Constructor of an object to dump mol2 files. :param AllInfo all_info: System information. :param str filename: Output file base name. .. py:function:: setChangeFreeType(string type) specifies the type of free particles which will be changed to be 'F' in output file. .. py:function:: deleteBoundaryBond(bool switch) switches on the function of screening the bonds across the box with 'True'. Example:: mol2 = gala.MOL2Dump(all_info, 'particles') mol2.setPeriod(100000) mol2.deleteBoundaryBond(True) app.add(mol2) XML dump -------- .. py:class:: XMLDump(all_info, filename) Constructor of an object to dump XML files. :param AllInfo all_info: System information. :param str filename: Output file base name. .. py:class:: XMLDump(all_info, group, filename) Constructor of an object to dump XML files for a group of particles. :param AllInfo all_info: System information. :param ParticleSet group: A group of particles. :param str filename: Output file base name. .. py:function:: setOutput(PyObject* out_put_list) indicates the output data type with the candidates:: ['position', 'type', 'velocity', 'mass', 'image', 'force', 'potential', 'virial', 'virial_matrix', 'charge', 'diameter', 'body', 'orientation', 'quaternion', 'rotation', 'rotangle', 'torque', 'inert', 'init', 'cris', 'molecule', 'bond', 'angle', 'dihedral', 'constraint', 'vsite'] Each data type also could be outputed by a single function as following. .. py:function:: setOutputPosition(bool switch) Outputs particle position (default value is true). .. py:function:: setOutputType (bool switch) Outputs particle type (default value is true). .. py:function:: setOutputImage(bool switch) Outputs particle image. .. py:function:: setOutputVelocity(bool switch) Outputs particle velocity. .. py:function:: setOutputMass(bool switch) Outputs particle mass. .. py:function:: setOutputCharge(bool switch) Outputs particle charge. .. py:function:: setOutputDiameter(bool switch) Outputs particle diameter. .. py:function:: setOutputBody(bool switch) Outputs particle body. .. py:function:: setOutputVirial(bool switch) Outputs particle virial. .. py:function:: setOutputForce(bool switch) Outputs particle force (x, y, z). .. py:function:: setOutputPotential(bool switch) Outputs particle potential. .. py:function:: setOutputOrientation(bool switch) Outputs particle orientation. .. py:function:: setOutputQuaternion(bool switch) Outputs particle quaternion. .. py:function:: setOutputRotation(bool switch) Outputs particle rotation velocity. .. py:function:: setOutputRotangle(bool switch) Outputs particle accumulated rotated angle at the direction of (0, 0, 1) in 3D or (0, 1, 0) in 2D. .. py:function:: setOutputTorque(bool switch) Outputs particle torque. .. py:function:: setOutputInert(bool switch) Outputs particle inert tensor. .. py:function:: setOutputInit(bool switch) Outputs particle initiator indicator. .. py:function:: setOutputCris(bool switch) Outputs particle cross-linking indicator. .. py:function:: setOutputBond(bool switch) Outputs bonds. .. py:function:: setOutputAngle(bool switch) Outputs angles. .. py:function:: setOutputDihedral(bool switch) Outputs dihedrals. .. py:function:: setOutputConstraint(bool switch) Outputs bond constraints. .. py:function:: setOutputVsite(bool switch) Outputs virual sites. .. py:function:: setOutputLocalForce(Force object) Outputs particle force(x, y, z and w where w is potential) of a Force object. .. py:function:: setOutputLocalVirial(Force object) Outputs particle virial of a Force object. .. py:function:: setOutputLocalVirialMatrix(Force object) Outputs particle virial matrix of a Force object. .. py:function:: setOutputPatch(AniForce object) outputs patch information for display in OVITO. .. py:function:: setOutputEllipsoid(BondForceHarmonicEllipsoid object) outputs ellipsoid bond information for display in OVITO. .. py:function:: setOutputEllipsoid(PBGBForce object) outputs ellipsoid information for display in OVITO. .. py:function:: setOutputEllipsoid(GBForce object) outputs ellipsoid information for display in OVITO. Example:: xml = gala.XMLDump(all_info, 'particles') xml.setOutput(['image', 'bond']) xml.setPeriod(100000) app.add(xml) DCD trajectory dump ------------------- .. py:class:: DCDDump(all_info, filename, overwrite) The constructor of a dump object of DCD file. :param AllInfo all_info: The system information. :param str filename: The output file name. :param bool overwrite: If overwrite the existed DCD file. .. py:class:: DCDDump(all_info, group, filename, overwrite) The constructor of a dump object of DCD file for a group of particles. :param AllInfo all_info: The system information. :param ParticleSet group: The group of particles. :param str filename: The output file name. :param bool overwrite: If overwrite the existed DCD file. .. py:function:: unpbc(bool switch) Outputs particle positions without the application of periodic boundary condition (PBC). Default value is False, i.e. with PBC condition. .. py:function:: unwrap(bool switch) Unwraps the molecules across box boundary due to PBC condition. Default value is False, i.e. wrapping molecules. Example:: dcd = gala.DCDDump(all_info, 'particles', True) dcd.unwrap(True) dcd.setPeriod(100000) app.add(dcd) Binary dump -------------------- .. py:class:: BinaryDump(all_info, filename) Constructor of an object to dump binary files. :param AllInfo all_info: System information. :param str filename: Output file base name. .. py:function:: setOutput(PyObject* out_put_list) indicates the output data type with the candidates:: ['position', 'type', 'velocity', 'mass', 'image', 'force', 'potential', 'virial', 'virial_matrix', 'charge', 'diameter', 'body', 'orientation', 'quaternion', 'rotation', 'rotangle', 'torque', 'inert', 'init', 'cris', 'molecule', 'bond', 'angle', 'dihedral', 'constraint', 'vsite'] .. py:function:: setOutputAll() Outputs all data. .. py:function:: setOutputForRestart() Outputs data needed for restarting. .. py:function:: enableCompression(bool switch) Compresses output file. Example:: binary = gala.BinaryDump(all_info, 'particle') binary.setOutput(['image', 'bond']) binary.setPeriod(10000) app.add(binary)