def _setOptimField(self, director, table, form):
"Special field: Optimization - depends on server"
# Explain link
visual_ = "material_simulations/espresso/link-opt"
explLink = director.retrieveVisual(visual_, form=form)
localdisk = FormCheckBox(name="localdisk", value=OPT_DEFAULT)
diskgrid = QEGrid(lc.grid())
diskgrid.addRow((localdisk, explLink))
table.addRow(("Optimization:", diskgrid.grid()))
def _setOptimField(self, director, table, form):
"Special field: Optimization - depends on server"
# Explain link
visual_ = "material_simulations/espresso/link-opt"
explLink = director.retrieveVisual(visual_, form=form)
localdisk = FormCheckBox(name="localdisk", value = OPT_DEFAULT)
diskgrid = QEGrid(lc.grid())
diskgrid.addRow((localdisk, explLink))
table.addRow(("Optimization:", diskgrid.grid()))
def _latticeTable(self, lp):
"Takes lattice parameters and returns formatted table of lattice structure"
if not self._output: # No output
return NONE
table = QEGrid(lc.grid(Class="qe-table-forces"))
table.addRow(("A", "B", "C", "cosAB", "cosAC", "cosBC"))
table.addRow(self._fstr(lp))
table.setRowStyle(0, "qe-table-header-left")
return table.grid()
def stress(self):
"Returns formatted stress"
if not self._output: # No output
return NONE
stress = self._outputStress()
if not stress: # No stress in the output
return NONE
table = QEGrid(lc.grid(Class="qe-table-stress"))
for s in stress:
table.addRow(("%.2f %.2f %.2f" % (s[0], s[1], s[2]) ))
return table.grid()
def stress(self):
"Returns formatted stress"
if not self._output: # No output
return NONE
stress = self._outputStress()
if not stress: # No stress in the output
return NONE
table = QEGrid(lc.grid(Class="qe-table-stress"))
for s in stress:
table.addRow(("%.2f %.2f %.2f" % (s[0], s[1], s[2])))
return table.grid()
def _latticeTable(self, lp):
"Takes lattice parameters and returns formatted table of lattice structure"
if not self._output: # No output
return NONE
table = QEGrid(lc.grid(Class="qe-table-forces"))
table.addRow(("A", "B", "C", "cosAB", "cosAC", "cosBC"))
table.addRow(self._fstr(lp))
table.setRowStyle(0, "qe-table-header-left")
return table.grid()
def _position(self, poslist):
"Returns formatted structure of atomic positions"
# Example: poslist = [('a', [0, 0, 0]), ('b', [1, 1, 1])]
if not self._output: # No output
return NONE
table = QEGrid(lc.grid(Class="qe-table-forces"))
table.addRow(("Atom", "Coordinates"))
for pl in poslist:
table.addRow(
(pl[0], "%.2f, %.2f, %.2f" % (pl[1][0], pl[1][1], pl[1][2])))
table.setRowStyle(0, "qe-table-header-left")
return table.grid()
def atomicStructure(self):
"Atom mass name: mass<number>, atom pseudo potential name: pseudo<number>"
atoms = QEGrid(lc.grid(Class="qe-table-atomic"))
list = self._atomsList()
if not list:
return NONE
atoms.addRow(
("Atom", "Position (bohr)", "Mass (u)", "Pseudo-Potential"))
for row in list:
atoms.addRow((row[1], row[2], row[3], row[4]))
atoms.setRowStyle(0, "qe-table-header-left")
return atoms.grid()
def _position(self, poslist):
"Returns formatted structure of atomic positions"
# Example: poslist = [('a', [0, 0, 0]), ('b', [1, 1, 1])]
if not self._output: # No output
return NONE
table = QEGrid(lc.grid(Class="qe-table-forces"))
table.addRow(("Atom", "Coordinates"))
for pl in poslist:
table.addRow((pl[0], "%.2f, %.2f, %.2f" % (pl[1][0], pl[1][1], pl[1][2])))
table.setRowStyle(0, "qe-table-header-left")
return table.grid()
def forces(self):
"Returns formatted force vector for each atom"
if not self._output: # No output
return NONE
forces = self._outputForces()
if not forces: # No forces in the output
return NONE
table = QEGrid(lc.grid(Class="qe-table-forces"))
table.addRow(("Atom", "Force (Ry/bohr)"))
for f in forces:
table.addRow((f[1], "%.2f, %.2f, %.2f" % (f[2], f[3], f[4])))
table.setRowStyle(0, "qe-table-header-left")
return table.grid()
def taskInfo(self):
table = QEGrid(lc.grid(Class="qe-tasks-info"))
if self._task: # If task exists
self._setTaskInfo(table) # Main scenario
return table.grid()
# No task created, show link "Create New Task"
link = lc.link(label="Create New Task",
onclick = load(actor = 'material_simulations/espresso/task-create',
routine = 'createRecord',
simid = self._simid,
tasktype = self._type,
linkorder = self._linkorder)
)
table.addRow((link, ))
#table.addRow(("or", )) # Keep
#table.addRow(("Use Existing Task", )) # Keep
return table.grid()
def tasks(self):
container = ""
simrecord = SimulationRecord(self._director, self._simid)
tasklist = simrecord.taskList()
if not tasklist:
return container
self._types = simrecord.typeList()
table = QEGrid(lc.grid(Class="qe-tasks-table"))
doshow = self._showActions(tasklist) # show "Run Task"?
for i in range(len(tasklist)):
rows = self._list(doshow)
self._setTaskCell(table, i, tasklist[i], rows)
if doshow:
# Special layout for action buttons (e.g. "Run Task")
table.setCellStyle(2, i, "qe-action-task")
return table.grid()
def atomicStructure(self):
"Atom mass name: mass<number>, atom pseudo potential name: pseudo<number>"
atoms = QEGrid(lc.grid(Class="qe-table-atomic"))
list = self._atomsList()
if not list:
return NONE
atoms.addRow(("Atom", "Position (bohr)", "Mass (u)", "Pseudo-Potential"))
for row in list:
atoms.addRow((row[1], row[2], row[3], row[4]))
atoms.setRowStyle(0, "qe-table-header-left")
return atoms.grid()
def forces(self):
"Returns formatted force vector for each atom"
if not self._output: # No output
return NONE
forces = self._outputForces()
if not forces: # No forces in the output
return NONE
table = QEGrid(lc.grid(Class="qe-table-forces"))
table.addRow(("Atom", "Force (Ry/bohr)"))
for f in forces:
table.addRow((f[1], "%.2f, %.2f, %.2f" % (f[2], f[3], f[4]) ))
table.setRowStyle(0, "qe-table-header-left")
return table.grid()
def taskInfo(self):
table = QEGrid(lc.grid(Class="qe-tasks-info"))
if self._task: # If task exists
self._setTaskInfo(table) # Main scenario
return table.grid()
# No task created, show link "Create New Task"
link = lc.link(label="Create New Task",
onclick=load(
actor='material_simulations/espresso/task-create',
routine='createRecord',
simid=self._simid,
tasktype=self._type,
linkorder=self._linkorder))
table.addRow((link, ))
#table.addRow(("or", )) # Keep
#table.addRow(("Use Existing Task", )) # Keep
return table.grid()
def _summary(self, director, section):
"System Summary"
section.add(lc.paragraph(text="System Summary", Class="qe-section"))
table = QEGrid(lc.grid(Class="qe-table-analysis"))
section.add(table.grid())
table.addRow(("Material Type:", self._pwresult.materialType()))
table.addRow(("Lattice Type:", self._pwresult.latticeType()))
table.addRow(
("Atomic Structure:", self._pwresult.atomicStructure()
)) # "# Atom Position (bohr) Mass (u) Pseudo-Potentials"
table.addRow(("Energy Cutoff:", self._pwresult.energyCutoff()))
table.addRow(("Density Cutoff:", self._pwresult.densityCutoff()))
if self._pwresult.materialType(
) == "Metal": # Parameters specific for metals
table.addRow(("Smearing Type:",
self._pwresult.smearingType())) # For metals only
table.addRow(("Smearing Degree:",
self._pwresult.smearingDegree())) # For metals only
table.addRow(("K points:", self._pwresult.kPoints()))
table.setColumnStyle(0, "qe-cell-param-analysis")
def _electronStructure(self, director, section):
"Electron Structure"
# output exists
section.add(lc.paragraph(text="Electron System", Class="qe-section"))
table = QEGrid(lc.grid(Class="qe-table-analysis"))
section.add(table.grid())
table.addRow(('Total Energy:', self._pwresult.totalEnergy(True)))
table.addRow(('Fermi Energy:', self._pwresult.fermiEnergy(True)))
table.addRow(("Forces:", self._pwresult.forces()))
table.addRow(("Stress (Ry/bohr^2):", self._pwresult.stress()))
table.setColumnStyle(0, "qe-cell-param-analysis")