Data output

Collective information

class DumpInfo(all_info, comp_info, filename)

The constructor of an information dump object of a group of particles.

Parameters:
  • all_info (AllInfo) – The system information.
  • comp_info (ComputeInfo) – The object of calculation of collective information.
  • filename (str) – The output file name.
dumpAnisotropy()

switches on the dump of information related to anisotropic particles.

dumpVirialEnergy(Force force)

switches on the dump of energy and virial of inputting force object.

Example:

dinfo = galamost.DumpInfo(all_info, comp_info, 'data.log')
dinfo.setPeriod(200)
app.add(dinfo)

MOL2 dump

class Mol2Dump(all_info, filename)

The constructor of a dump object of mol2 files.

Parameters:
  • all_info (AllInfo) – The system information.
  • filename (str) – The output file base name.
setChangeFreeType(string type)

specifies the type of free particles which will be changed to be ‘F’ in output file.

deleteBoundaryBond(bool switch)

switches on the function of not displaying the bonds across the box.

Example:

mol2 = galamost.Mol2Dump(all_info, 'particles')
mol2.setPeriod(100000)
mol2.deleteBoundaryBond(True)
app.add(mol2)

XML dump

class XmlDump(all_info, filename)

The constructor of a dump object of XML files.

Parameters:
  • all_info (AllInfo) – The system information.
  • filename (str) – The output file name.
class XmlDump(all_info, group, filename)

The constructor of a dump object of XML files for a group of particles.

Parameters:
  • all_info (AllInfo) – The system information.
  • group (ParticleSet) – The group of particles.
  • filename (str) – The output file base name.
setOutput(PyObject* out_put_list)

indicate the output data type.

setOutputPosition(bool switch)

switches the function of output position (the default is true).

setOutputType(bool switch)

switches the function of output type (the default is true).

setOutputImage(bool switch)

switches the function of output image.

setOutputVelocity(bool switch)

switches the function of output velocity.

setOutputMass(bool switch)

switches the function of output mass.

setOutputCharge(bool switch)

switchesthe function of output charge.

setOutputDiameter(bool switch)

switches the function of output diameter.

setOutputBody(bool switch)

switches the function of output body.

setOutputVirial(bool switch)

switches the function of output virial.

setOutputForce(bool switch)

switches the function of output force.

setOutputOrientation(bool switch)

switches the function of output orientation.

setOutputQuaternion(bool switch)

switches the function of output quaternion.

setOutputRotation(bool switch)

switches the function of output rotation velocity.

setOutputTorque(bool switch)

switches the function of output torque.

setOutputInert(bool switch)

switches the function of output inert tensor.

setOutputInit(bool switch)

switches the function of output initiator indication.

setOutputCris(bool switch)

switches the function of output cris.

setOutputBond(bool switch)

switches the function of output bond.

setOutputAngle(bool switch)

switches the function of output angle.

setOutputDihedral(bool switch)

switches the function of output dihedral.

setOutputEllipsoid(PBGBForce object)

outputs ellipsoid information for display in OVITO.

setOutputEllipsoid(GBForce object)

outputs ellipsoid information for display in OVITO.

Example:

xml = galamost.XmlDump(all_info, 'particles')
xml.setOutput(['image', 'bond '])
xml.setPeriod(100000)
app.add(xml)

DCD trajectory dump

class DcdDump(all_info, filename, overwrite)

The constructor of a dump object of DCD file.

Parameters:
  • all_info (AllInfo) – The system information.
  • filename (str) – The output file name.
  • overwrite (bool) – If overwrite the existed DCD file.
class DcdDump(all_info, group, filename, overwrite)

The constructor of a dump object of DCD file for a group of particles.

Parameters:
  • all_info (AllInfo) – The system information.
  • group (ParticleSet) – The group of particles.
  • filename (str) – The output file name.
  • overwrite (bool) – If overwrite the existed DCD file.
unpbc(bool switch)

switches the function of outputing the particle position without the application of PBC, the default value is false.

unwrap(bool switch)

switches the function of unwrapping the molecules across box boundary due to PBC condition, the default value is false.

Example:

dcd = galamost.DcdDump(all_info, 'particles',True)
dcd.unwrap(True)
dcd.setPeriod(100000)
app.add(dcd)

GALAMOST binary dump

class BinaryDump(all_info, filename)

The constructor of a dump object of GALAMOST binary file.

Parameters:
  • all_info (AllInfo) – The system information.
  • filename (str) – The output file base name.
setOutputAll()

switches on the function of output all data.

setOutputForRestart()

switches on the function of output data needed for restarting.

enableCompression(bool switch)

switches the function of compressing output file.

Example:

binary = galamost.BinaryDump(all_info, 'particle')
binary.setOutput(['image', 'bond'])
binary.setPeriod(10000)
app.add(binary)