def __init__(self, job_parms, **job_prop):
"""
To support the 2 ways of gamess job creation.
"""
name = "Gamess Job 1"
[self.job_batfile, self.job_outputfile] = job_prop.get('job_from_file', [None, None])
if self.job_outputfile:
self.job_outputfile = self.job_outputfile.strip('"')
self.gamessJig = job_prop.get('jig', None)
if self.job_batfile:
server_id = job_parms['Server_id']
self.server = ServerManager().getServerById(int(server_id))
if not self.server:
raise ValueError, "The server of %d can't be found." % server_id
SimJob.__init__(self, name, job_parms)
self.edit_cntl = GamessProp()
#Huaicai 7/6/05: try to fix the problem when run a gamess jig coming from mmp file
#and without opening the jig property windows and save it.
if not self.__dict__.has_key('server'):
sManager = ServerManager()
self.server = sManager.getServers()[0]
return
def __init__(self, job_parms, **job_prop):
"""
To support the 2 ways of gamess job creation.
"""
name = "Gamess Job 1"
[self.job_batfile,
self.job_outputfile] = job_prop.get('job_from_file', [None, None])
if self.job_outputfile:
self.job_outputfile = self.job_outputfile.strip('"')
self.gamessJig = job_prop.get('jig', None)
if self.job_batfile:
server_id = job_parms['Server_id']
self.server = ServerManager().getServerById(int(server_id))
if not self.server:
raise ValueError, "The server of %d can't be found." % server_id
SimJob.__init__(self, name, job_parms)
self.edit_cntl = GamessProp()
#Huaicai 7/6/05: try to fix the problem when run a gamess jig coming from mmp file
#and without opening the jig property windows and save it.
if not self.__dict__.has_key('server'):
sManager = ServerManager()
self.server = sManager.getServers()[0]
return
def __init__(self):
QDialog.__init__(self)
self.setModal(True)
self.setupUi(self)
self.ecm_btngrp = QButtonGroup()
self.ecm_btngrp.setExclusive(True)
objId = 0
for obj in self.ecm_grpbox.children():
if isinstance(obj, QAbstractButton):
self.ecm_btngrp.addButton(obj)
self.ecm_btngrp.setId(obj, objId)
objId +=1
self.scftyp_btngrp = QButtonGroup()
self.scftyp_btngrp.setExclusive(True)
objId = 0
for obj in self.scftyp_grpbox.children():
if isinstance(obj, QAbstractButton):
self.scftyp_btngrp.addButton(obj)
self.scftyp_btngrp.setId(obj, objId)
objId +=1
self.connect(self.cancel_btn,SIGNAL("clicked()"),self.reject)
self.connect(self.ecm_btngrp,SIGNAL("buttonPressed(int)"),self.set_ecmethod)
self.connect(self.multi_combox,SIGNAL("activated(int)"),self.set_multiplicity)
self.connect(self.run_job_btn,SIGNAL("clicked()"),self.run_job)
self.connect(self.save_btn,SIGNAL("clicked()"),self.accept)
self.connect(self.runtyp_combox,SIGNAL("activated(int)"),self.calculate_changed)
self.connect(self.choose_color_btn,SIGNAL("clicked()"),self.change_jig_color)
self.connect(self.whats_this_btn,SIGNAL("clicked()"),self.whats_this)
##self.connect(self.new_btn,SIGNAL("clicked()"),self.addServer)
##self.connect(self.exit_btn,SIGNAL("clicked()"),self.close)
##self.connect(self.server_listview,SIGNAL("currentChanged(QListViewItem*)"),self.changeServer)
##self.connect(self.engine_combox,SIGNAL("activated(const QString&)"),self.engineChanged)
##self.connect(self.del_btn,SIGNAL("clicked()"),self.deleteServer)
self.sManager = ServerManager()
self.servers = self.sManager.getServers()
self.server = self.servers[0]
self.name_linedit.setWhatsThis("""Name of the GAMESS jig.""")
self.runtyp_combox.setWhatsThis("""Type of calculation, where "Energy" calculates the Energy Minima,and "Optimization" calculates the "Equilibrium Geometry".""")
self.comment_linedit.setWhatsThis("""Description, also placed in the comment line of the $DATA section of the INP file.""")
self.choose_color_btn.setWhatsThis("""Change the GAMESS jig color.""")
self.rhf_radiobtn.setWhatsThis("""Restricted Hartree-Fock. All electrons are paired and each spatial orbital is doubly occupied. Cannot be used with multiplicities greater than 1.""")
self.uhf_radiobtn.setWhatsThis("""Unrestricted Hartree-Fock. All electrons are unpaired and spatial (spin) orbitals are uniquely defined for each electron. More time consuming, but more accurate, than ROHF. """)
self.rohf_radiobtn.setWhatsThis("""Restricted Open-shell Hartree-Fock. Spin-paired electrons are assigned to doubly-occupied spatial orbitals, while electrons with unpaired spins are provided unique spatial orbitals.""")
self.icharg_spinbox.setWhatsThis("""The total charge of the structure to be treated quantum mechanically (ICHARG).""")
self.multi_combox.setWhatsThis("""N + 1, where N is the number of unpaired electrons (MULT).""")
self.memory_spinbox.setWhatsThis("""System memory reserved for calculation""")
self.dirscf_checkbox.setWhatsThis("""Check this box to run the calculation in RAM and avoid hard disk usage for integral storage.""")
self.gbasis_combox.setWhatsThis("""Select from among the standard Gaussian-type basis sets and semi-empirical parameters in GAMESS.""")
self.checkBox10_3_2.setWhatsThis("""Reads the $HESS group from the output file of a previous GAMESS calculation. Only valid for identical molecules.""")
self.checkBox10_2_2_2.setWhatsThis("""Reads the $VEC group from the output of a previous GAMESS calculation. Requires that both the molecule and basis set be identical. Useful for restarted calculations and starting orbitals for electron correlation methods.""")
self.none_radiobtn.setWhatsThis("""Select this button to neglect electron correlation in the calculation.""")
self.dft_radiobtn.setWhatsThis("""Select this button to perform a density functional theory calculation.""")
self.mp2_radiobtn.setWhatsThis("""Select this button to perform a Second-Order Moeller Plesset calculation.""")
self.dfttyp_combox.setWhatsThis("""Select an available density functional in GAMESS.""")
self.gridsize_combox.setWhatsThis("""Select the grid spacing for the DFT calculation.""")
self.core_electrons_checkbox.setWhatsThis("""Check this box to include both the valence and core electrons in the MP2 calculation.""")
self.density_conv_combox.setWhatsThis("""Selects the accuracy of the electron density convergence for the calculation (CONV).""")
self.rmsd_combox.setWhatsThis("""Gradient convergence tolerance (OPTTOL), in Hartree/Bohr. Convergence of a geometry search requires the largest component of the gradient to be less than this value, and the root mean square gradient less than 1/3 of OPTTOL. (default=0.0001)""")
self.iterations_spinbox.setWhatsThis("""Maximum number of SCF iteration cycles (MAXIT).""")
self.edit_input_file_cbox.setWhatsThis("""Opens the INP file generated by NanoEngineer-1 in a text editor.""")
self.whats_this_btn.setWhatsThis("""What's This Help Utility""")
self.run_job_btn.setWhatsThis("""Save GAMESS parameters, generates the INP file and launches the GAMESS job.""")
self.save_btn.setWhatsThis("""Save GAMESS parameters and generates the INP file. It does not launch the GAMESS job.""")
self.cancel_btn.setWhatsThis("""Cancels changes and closes dialog.""")
class GamessProp(QDialog, Ui_GamessPropDialog):
"""
The Gamess Jig Properties dialog used for:
- running a GAMESS energy calculation on a structure (group of atoms).
- running a GAMESS optimization on a structure.
- setting and saving the GAMESS parameters used for an energy calculation or optimization.
"""
def __init__(self):
QDialog.__init__(self)
self.setModal(True)
self.setupUi(self)
self.ecm_btngrp = QButtonGroup()
self.ecm_btngrp.setExclusive(True)
objId = 0
for obj in self.ecm_grpbox.children():
if isinstance(obj, QAbstractButton):
self.ecm_btngrp.addButton(obj)
self.ecm_btngrp.setId(obj, objId)
objId +=1
self.scftyp_btngrp = QButtonGroup()
self.scftyp_btngrp.setExclusive(True)
objId = 0
for obj in self.scftyp_grpbox.children():
if isinstance(obj, QAbstractButton):
self.scftyp_btngrp.addButton(obj)
self.scftyp_btngrp.setId(obj, objId)
objId +=1
self.connect(self.cancel_btn,SIGNAL("clicked()"),self.reject)
self.connect(self.ecm_btngrp,SIGNAL("buttonPressed(int)"),self.set_ecmethod)
self.connect(self.multi_combox,SIGNAL("activated(int)"),self.set_multiplicity)
self.connect(self.run_job_btn,SIGNAL("clicked()"),self.run_job)
self.connect(self.save_btn,SIGNAL("clicked()"),self.accept)
self.connect(self.runtyp_combox,SIGNAL("activated(int)"),self.calculate_changed)
self.connect(self.choose_color_btn,SIGNAL("clicked()"),self.change_jig_color)
self.connect(self.whats_this_btn,SIGNAL("clicked()"),self.whats_this)
##self.connect(self.new_btn,SIGNAL("clicked()"),self.addServer)
##self.connect(self.exit_btn,SIGNAL("clicked()"),self.close)
##self.connect(self.server_listview,SIGNAL("currentChanged(QListViewItem*)"),self.changeServer)
##self.connect(self.engine_combox,SIGNAL("activated(const QString&)"),self.engineChanged)
##self.connect(self.del_btn,SIGNAL("clicked()"),self.deleteServer)
self.sManager = ServerManager()
self.servers = self.sManager.getServers()
self.server = self.servers[0]
self.name_linedit.setWhatsThis("""Name of the GAMESS jig.""")
self.runtyp_combox.setWhatsThis("""Type of calculation, where "Energy" calculates the Energy Minima,and "Optimization" calculates the "Equilibrium Geometry".""")
self.comment_linedit.setWhatsThis("""Description, also placed in the comment line of the $DATA section of the INP file.""")
self.choose_color_btn.setWhatsThis("""Change the GAMESS jig color.""")
self.rhf_radiobtn.setWhatsThis("""Restricted Hartree-Fock. All electrons are paired and each spatial orbital is doubly occupied. Cannot be used with multiplicities greater than 1.""")
self.uhf_radiobtn.setWhatsThis("""Unrestricted Hartree-Fock. All electrons are unpaired and spatial (spin) orbitals are uniquely defined for each electron. More time consuming, but more accurate, than ROHF. """)
self.rohf_radiobtn.setWhatsThis("""Restricted Open-shell Hartree-Fock. Spin-paired electrons are assigned to doubly-occupied spatial orbitals, while electrons with unpaired spins are provided unique spatial orbitals.""")
self.icharg_spinbox.setWhatsThis("""The total charge of the structure to be treated quantum mechanically (ICHARG).""")
self.multi_combox.setWhatsThis("""N + 1, where N is the number of unpaired electrons (MULT).""")
self.memory_spinbox.setWhatsThis("""System memory reserved for calculation""")
self.dirscf_checkbox.setWhatsThis("""Check this box to run the calculation in RAM and avoid hard disk usage for integral storage.""")
self.gbasis_combox.setWhatsThis("""Select from among the standard Gaussian-type basis sets and semi-empirical parameters in GAMESS.""")
self.checkBox10_3_2.setWhatsThis("""Reads the $HESS group from the output file of a previous GAMESS calculation. Only valid for identical molecules.""")
self.checkBox10_2_2_2.setWhatsThis("""Reads the $VEC group from the output of a previous GAMESS calculation. Requires that both the molecule and basis set be identical. Useful for restarted calculations and starting orbitals for electron correlation methods.""")
self.none_radiobtn.setWhatsThis("""Select this button to neglect electron correlation in the calculation.""")
self.dft_radiobtn.setWhatsThis("""Select this button to perform a density functional theory calculation.""")
self.mp2_radiobtn.setWhatsThis("""Select this button to perform a Second-Order Moeller Plesset calculation.""")
self.dfttyp_combox.setWhatsThis("""Select an available density functional in GAMESS.""")
self.gridsize_combox.setWhatsThis("""Select the grid spacing for the DFT calculation.""")
self.core_electrons_checkbox.setWhatsThis("""Check this box to include both the valence and core electrons in the MP2 calculation.""")
self.density_conv_combox.setWhatsThis("""Selects the accuracy of the electron density convergence for the calculation (CONV).""")
self.rmsd_combox.setWhatsThis("""Gradient convergence tolerance (OPTTOL), in Hartree/Bohr. Convergence of a geometry search requires the largest component of the gradient to be less than this value, and the root mean square gradient less than 1/3 of OPTTOL. (default=0.0001)""")
self.iterations_spinbox.setWhatsThis("""Maximum number of SCF iteration cycles (MAXIT).""")
self.edit_input_file_cbox.setWhatsThis("""Opens the INP file generated by NanoEngineer-1 in a text editor.""")
self.whats_this_btn.setWhatsThis("""What's This Help Utility""")
self.run_job_btn.setWhatsThis("""Save GAMESS parameters, generates the INP file and launches the GAMESS job.""")
self.save_btn.setWhatsThis("""Save GAMESS parameters and generates the INP file. It does not launch the GAMESS job.""")
self.cancel_btn.setWhatsThis("""Cancels changes and closes dialog.""")
def showDialog(self, job):
"""
Display the GAMESS Jig Properties dialog
"""
self.gamessJig = job.gamessJig
self.job = job
self.pset = self.gamessJig.pset
self.win = self.gamessJig.assy.w
self.glpane = self.gamessJig.assy.o
if self._setup(): return
self.exec_()
######Private or helper methods###############################
def _setup(self):
"""
Setup widgets to initial (default or defined) values. Return True on error.
"""
#To fix bug 684
#if gamess.is_disabled():
# self.run_job_btn.setEnabled(False)
#else:
# self.run_job_btn.setEnabled(True)
self.jig_attrs = self.gamessJig.copyable_attrs_dict() # Save the jig's attributes in case of Cancel.
# Jig color
self.original_normcolor = self.gamessJig.normcolor
self.jig_QColor = RGBf_to_QColor(self.gamessJig.normcolor) # Used as default color by Color Chooser
self.jig_color_pixmap = get_widget_with_color_palette(
self.jig_color_pixmap, self.jig_QColor)
# Init the top widgets (name, runtyp drop box, comment)
self.name_linedit.setText(self.gamessJig.name)
self.runtyp_combox.setCurrentIndex(self.pset.ui.runtyp) # RUNTYP
self.calculate_changed(self.pset.ui.runtyp)
self.comment_linedit.setText(self.pset.ui.comment)
# Electronic Structure Properties section.
btn = self.scftyp_btngrp.button(self.pset.ui.scftyp)# RHF, UHF, or ROHF
btn.setChecked(True)
self.icharg_spinbox.setValue(self.pset.ui.icharg) # Charge
self.multi_combox.setCurrentIndex(self.pset.ui.mult) # Multiplicity
# Disable RHF if multiplicity is not the first item.
if self.pset.ui.mult == 0:
self.rhf_radiobtn.setEnabled(1) # Enable RHF
else:
self.rhf_radiobtn.setEnabled(0) # Disable RHF
# System Memory and Usage
self.dirscf_checkbox.setChecked(self.pset.ui.dirscf) # DIRSCF
self.memory_spinbox.setValue(self.pset.ui.memory) # Memory
# Electron Correlation Method and Basis Set
ecm = self.pset.ui.ecm
btn = self.ecm_btngrp.button(self.pset.ui.ecm)# None, DFT or MP2
btn.setChecked(True)
self.set_ecmethod(self.pset.ui.ecm) # None, DFT or MP2
self.gbasis_combox.setCurrentIndex(self.pset.ui.gbasis) # Basis set
# Load the combo box with all the valid DFT functions.
self._load_dfttyp_combox()
self.dfttyp_combox.setCurrentIndex(self.pset.ui.dfttyp) # DFT Functional
self.gridsize_combox.setCurrentIndex(self.pset.ui.gridsize) # Grid Size
self.core_electrons_checkbox.setChecked(self.pset.ui.ncore) # Include core electrons
# Convergence Criteria
self.density_conv_combox.setCurrentIndex(self.pset.ui.conv) # Density Convergence
self.rmsd_combox.setCurrentIndex(self.pset.ui.rmsdconv) # RMSD Convergence
self.iterations_spinbox.setValue(self.pset.ui.iterations) # Iterations
# These have been removed per discussions with Damian.
# Mark 050628
# self.extrap_checkbox.setChecked(self.pset.ui.extrap) # EXTRAP
# self.damp_checkbox.setChecked(self.pset.ui.damp) # DAMP
# self.diis_checkbox.setChecked(self.pset.ui.diis) # DIIS
# self.shift_checkbox.setChecked(self.pset.ui.shift) # SHIFT
# self.soscf_checkbox.setChecked(self.pset.ui.soscf) # SOSCF
# self.rstrct_checkbox.setChecked(self.pset.ui.rstrct) # RSTRCT
# Load the server combo box
#self._reloadServerList() # Not used in A6. Mark.
# If there is an error, return 1. NIY.
return 0
def _reloadServerList(self):
"""
Load the server combo box
"""
self.server_combox.clear()
for s in self.servers:
self.server_combox.insertItem(100, s.hostname + "-" + s.engine)
# 100 makes sure item is appended to list. [mark 2007-05-04]
if self.server not in self.servers:
self.server = self.servers[0]
indx = self.servers.index(self.server)
self.server_combox.setCurrentIndex(indx)
def _load_dfttyp_combox(self):
"""
Load list of DFT function in a combobox widget
"""
self.dfttyp_combox.clear() # Clear all combo box items
if self.server.engine == 'GAMESS':
for f in gms_dfttyp_items:
self.dfttyp_combox.insertItem(100, f)
# 100 makes sure item is appended to list. [mark 2007-05-04]
elif self.server.engine == 'PC GAMESS':
for f in pcgms_dfttyp_items:
self.dfttyp_combox.insertItem(100, f)
# 100 makes sure item is appended to list. [mark 2007-05-04]
else:
print "load_dfttyp_combox: Unknown GAMESS Version. Loading GAMES DFT functionals."
for f in gms_dfttyp_items:
self.dfttyp_combox.insertItem(100, f)
# 100 makes sure item is appended to list. [mark 2007-05-04]
def _update_gbasis_list(self, val):
"""
Add/remove AM1 and PM3 to/from the gbasis list.
"""
citem = self.gbasis_combox.currentIndex()
if val == DFT or val == MP2:
if self.gbasis_combox.count() == 18:
self.gbasis_combox.removeItem(0)
self.gbasis_combox.removeItem(0)
self.gbasis_combox.setCurrentIndex(max(0, citem-2))
else:
if self.gbasis_combox.count() != 18:
self.gbasis_combox.insertItem(0,"PM3") # 0 prepends item to list.
self.gbasis_combox.insertItem(0,"AM1")
self.gbasis_combox.setCurrentIndex(citem+2)
def _save_ui_settings(self):
"""
Save the UI settings in the Gamess jig pset.
There is one setting for each pset.
"""
self.pset.ui.comment = str(self.comment_linedit.text()) # Description
self.pset.ui.runtyp = self.runtyp_combox.currentIndex() # RUNTYP = Energy or Optimize
# Electronic Structure Props and Basis Set section.
self.pset.ui.scftyp = self.scftyp_btngrp.checkedId() # SCFTYP = RHF, UHF, or ROHF
self.pset.ui.icharg = self.icharg_spinbox.value() # Charge
self.pset.ui.mult = self.multi_combox.currentIndex() # Multiplicity
# System Memory and Usage
self.pset.ui.memory = self.memory_spinbox.value() # Memory
self.pset.ui.dirscf = self.dirscf_checkbox.isChecked() # DIRSCF
# Electron Correlation Method
self.pset.ui.ecm = self.ecm_btngrp.checkedId() # None, DFT or MP2
#self.pset.ui.inttyp = self.ecm_btngrp.selectedId() # INTTYP
self.pset.ui.gbasis = self.gbasis_combox.currentIndex() # Basis Set
self.pset.ui.gbasisname = str(self.gbasis_combox.currentText())
self.pset.ui.dfttyp = self.dfttyp_combox.currentIndex() # DFT Functional Type
self.pset.ui.gridsize = self.gridsize_combox.currentIndex() # Grid Size
self.pset.ui.ncore = self.core_electrons_checkbox.isChecked() # Include core electrons
# Convergence Criteria
self.pset.ui.conv = self.density_conv_combox.currentIndex() # Density Convergence
self.pset.ui.rmsdconv = self.rmsd_combox.currentIndex() # RMSD Convergence
self.pset.ui.iterations = self.iterations_spinbox.value() # Iterations
# self.pset.ui.extrap = self.extrap_checkbox.isChecked() # EXTRAP
# self.pset.ui.damp = self.damp_checkbox.isChecked() # DAMP
# self.pset.ui.diis = self.diis_checkbox.isChecked() # DIIS
# self.pset.ui.shift = self.shift_checkbox.isChecked() # SHIFT
# self.pset.ui.soscf = self.soscf_checkbox.isChecked() # SOSCF
# self.pset.ui.rstrct = self.rstrct_checkbox.isChecked() # RSTRCT
def _save_job_parms(self):
calculate = ['Energy', 'Optimization']
self.job.Calculation = calculate[self.pset.ui.runtyp]
self.job.Description = self.pset.ui.comment
self.job.server = self.server
##Copy some attributes from the server object to job description
self.job.Server_id = self.server.server_id
self.job.Engine = self.server.engine
######End of private or helper methods.########################
###### Unused methods ###############
def openServerManager(self):
"""
Pop up ServerManagerDialog to edit the properties of the servers.
"""
self.sManager.showDialog(self.server)
self.servers = self.sManager.getServers()
self._reloadServerList()
def serverChanged(self, si):
"""
User has changed server, so update the DFT comboBox. Currently not used.
"""
self.server = self.servers[si]
self._load_dfttyp_combox()
###### End of unused methods ###############
##########Slot methods for some GUI controls################
def calculate_changed(self, val):
"""
"""
if val == 0: # Energy
self.rmsd_lbl.setEnabled(0)
self.rmsd_combox.setEnabled(0)
self.iterations_lbl.setEnabled(0)
self.iterations_spinbox.setEnabled(0)
# self.extrap_checkbox.setEnabled(0)
# self.rstrct_checkbox.setEnabled(0)
# self.damp_checkbox.setEnabled(0)
# self.diis_checkbox.setEnabled(0)
# self.shift_checkbox.setEnabled(0)
# self.soscf_checkbox.setEnabled(0)
else: # Optimization
self.rmsd_lbl.setEnabled(1)
self.rmsd_combox.setEnabled(1)
self.iterations_lbl.setEnabled(1)
self.iterations_spinbox.setEnabled(1)
# self.extrap_checkbox.setEnabled(1)
# self.rstrct_checkbox.setEnabled(1)
# self.damp_checkbox.setEnabled(1)
# self.diis_checkbox.setEnabled(1)
# self.shift_checkbox.setEnabled(1)
# self.soscf_checkbox.setEnabled(1)
def set_multiplicity(self, val):
"""
Enable/disable widgets when user changes Multiplicity.
"""
if val != 0:
qt4todo("if scftyp[self.scftyp_btngrp.selectedId()] != 'RHF':")
#if scftyp[self.scftyp_btngrp.selectedId()] != 'RHF':
# self.rhf_radiobtn.setEnabled(0)
# return
ret = QMessageBox.warning( self, "Multiplicity Conflict",
"If Multiplicity is greater than 1, then <b>UHF</b> or <b>ROHF</b> must be selected.\n"
"Select Cancel to keep <b>RHF</b>.",
"&UHF", "&ROHF", "Cancel",
0, 2 )
if ret == 0: # UHF
self.uhf_radiobtn.toggle()
self.rhf_radiobtn.setEnabled(0)
elif ret == 1: # ROHF
self.rohf_radiobtn.toggle()
self.rhf_radiobtn.setEnabled(0)
elif ret == 2: # Cancel
self.multi_combox.setCurrentIndex(0)
elif val == 0:
self.rhf_radiobtn.setEnabled(1)
def set_ecmethod(self, val):
"""
Enable/disable widgets when user changes Electron Correlation Method.
"""
#print "set_ecmethod = ", val
if val == DFT:
self.dfttyp_label.setEnabled(1)
self.dfttyp_combox.setEnabled(1)
self.gridsize_label.setEnabled(1)
self.gridsize_combox.setEnabled(1)
self.core_electrons_checkbox.setChecked(0)
self.core_electrons_checkbox.setEnabled(0)
elif val == MP2:
self.core_electrons_checkbox.setEnabled(1)
self.dfttyp_label.setEnabled(0)
self.dfttyp_combox.setEnabled(0)
self.gridsize_label.setEnabled(0)
self.gridsize_combox.setEnabled(0)
else: # None = Hartree-Fock
self.dfttyp_label.setEnabled(0)
self.dfttyp_combox.setEnabled(0)
self.gridsize_label.setEnabled(0)
self.gridsize_combox.setEnabled(0)
self.core_electrons_checkbox.setChecked(0)
self.core_electrons_checkbox.setEnabled(0)
# AM1 and PM3 are not options for DFT or MP2.
# We have to remove or add them from the combo box.
self._update_gbasis_list(val)
def open_tmp_inputfile(self):
"""
Writes a temporary GAMESS inputfile of the current Gamess jig and opens the
file in an editor.
"""
# Make tmp_inputfile filename (i.e. ~/Nanorex/temp/jigname_parms_info.inp)
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
tmpdir = find_or_make_Nanorex_subdir('temp')
basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info('_')
tmp_inputfile = os.path.join(tmpdir, "%s.inp" % basename)
# Write INP file (in ~/Nanorex/temp subdirectory)
from analysis.GAMESS.files_gms import writegms_inpfile
writegms_inpfile(tmp_inputfile, self.gamessJig)
from platform_dependent.PlatformDependent import open_file_in_editor
open_file_in_editor(tmp_inputfile)
def run_job(self):
"""
Slot method for the 'Save and Run' button
"""
self.accept()
# Run GAMESS job. Return value r:
# 0 = success
# 1 = job cancelled
# 2 = job failed.
r = self.job.launch()
if r == 1: # Job was cancelled
env.history.message( redmsg( "GAMESS job cancelled."))
return
if r == 2: # Job failed.
env.history.message( redmsg( "GAMESS job failed. Maybe you didn't set the right Gamess executable file. Make sure you can run the same job manually."))
return
# Job success.
fn = self.gamessJig.outputfile
# Print energy or move atoms
if self.pset.ui.runtyp == 0: #Energy
self.gamessJig.print_energy()
else: # Optimize
try:
r = self.gamessJig.move_optimized_atoms()
# r = insertgms(self.gamessJig.assy, fn)
except:
print_compact_traceback( "GamessProp.run_job(): error reading GAMESS OUT file [%s]: " % fn )
env.history.message( redmsg( "Internal error while inserting GAMESS geometry: " + fn) )
else:
if r:
env.history.message(redmsg( "Atoms not adjusted."))
else:
self.gamessJig.assy.changed() # The file and the part are not the same.
self.gamessJig.print_energy() # Print the final energy from the optimize OUT file, too.
env.history.message( "Atoms adjusted.")
def change_jig_color(self):
"""
Slot method to change the jig's color.
"""
color = QColorDialog.getColor(self.jig_QColor, self)
if color.isValid():
self.jig_QColor = color
self.jig_color_pixmap = get_widget_with_color_palette(
self.jig_color_pixmap, self.jig_QColor)
self.gamessJig.color = self.gamessJig.normcolor = QColor_to_RGBf(color)
self.glpane.gl_update()
def accept(self):
"""
The slot method for the 'Save' button.
"""
QDialog.accept(self)
self.gamessJig.try_rename(self.name_linedit.text())
self._save_ui_settings()
self.gamessJig.update_gamess_parms() # Update all the GAMESS parameters.
self._save_job_parms()
if self.edit_input_file_cbox.isChecked():
self.open_tmp_inputfile()
def reject(self):
"""
The slot method for the 'Cancel' button.
"""
QDialog.reject(self)
self.gamessJig.attr_update(self.jig_attrs) # Restore attributes of the jig.
# self.gamessJig.color = self.gamessJig.normcolor = self.original_normcolor
self.gamessJig.cancelled = True
self.glpane.gl_update()
def whats_this(self):
from PyQt4.Qt import QWhatsThis, QDialog
QWhatsThis.enterWhatsThisMode()
def __init__(self):
QDialog.__init__(self)
self.setModal(True)
self.setupUi(self)
self.ecm_btngrp = QButtonGroup()
self.ecm_btngrp.setExclusive(True)
objId = 0
for obj in self.ecm_grpbox.children():
if isinstance(obj, QAbstractButton):
self.ecm_btngrp.addButton(obj)
self.ecm_btngrp.setId(obj, objId)
objId += 1
self.scftyp_btngrp = QButtonGroup()
self.scftyp_btngrp.setExclusive(True)
objId = 0
for obj in self.scftyp_grpbox.children():
if isinstance(obj, QAbstractButton):
self.scftyp_btngrp.addButton(obj)
self.scftyp_btngrp.setId(obj, objId)
objId += 1
self.connect(self.cancel_btn, SIGNAL("clicked()"), self.reject)
self.connect(self.ecm_btngrp, SIGNAL("buttonPressed(int)"),
self.set_ecmethod)
self.connect(self.multi_combox, SIGNAL("activated(int)"),
self.set_multiplicity)
self.connect(self.run_job_btn, SIGNAL("clicked()"), self.run_job)
self.connect(self.save_btn, SIGNAL("clicked()"), self.accept)
self.connect(self.runtyp_combox, SIGNAL("activated(int)"),
self.calculate_changed)
self.connect(self.choose_color_btn, SIGNAL("clicked()"),
self.change_jig_color)
self.connect(self.whats_this_btn, SIGNAL("clicked()"), self.whats_this)
##self.connect(self.new_btn,SIGNAL("clicked()"),self.addServer)
##self.connect(self.exit_btn,SIGNAL("clicked()"),self.close)
##self.connect(self.server_listview,SIGNAL("currentChanged(QListViewItem*)"),self.changeServer)
##self.connect(self.engine_combox,SIGNAL("activated(const QString&)"),self.engineChanged)
##self.connect(self.del_btn,SIGNAL("clicked()"),self.deleteServer)
self.sManager = ServerManager()
self.servers = self.sManager.getServers()
self.server = self.servers[0]
self.name_linedit.setWhatsThis("""Name of the GAMESS jig.""")
self.runtyp_combox.setWhatsThis(
"""Type of calculation, where "Energy" calculates the Energy Minima,and "Optimization" calculates the "Equilibrium Geometry"."""
)
self.comment_linedit.setWhatsThis(
"""Description, also placed in the comment line of the $DATA section of the INP file."""
)
self.choose_color_btn.setWhatsThis("""Change the GAMESS jig color.""")
self.rhf_radiobtn.setWhatsThis(
"""Restricted Hartree-Fock. All electrons are paired and each spatial orbital is doubly occupied. Cannot be used with multiplicities greater than 1."""
)
self.uhf_radiobtn.setWhatsThis(
"""Unrestricted Hartree-Fock. All electrons are unpaired and spatial (spin) orbitals are uniquely defined for each electron. More time consuming, but more accurate, than ROHF. """
)
self.rohf_radiobtn.setWhatsThis(
"""Restricted Open-shell Hartree-Fock. Spin-paired electrons are assigned to doubly-occupied spatial orbitals, while electrons with unpaired spins are provided unique spatial orbitals."""
)
self.icharg_spinbox.setWhatsThis(
"""The total charge of the structure to be treated quantum mechanically (ICHARG)."""
)
self.multi_combox.setWhatsThis(
"""N + 1, where N is the number of unpaired electrons (MULT).""")
self.memory_spinbox.setWhatsThis(
"""System memory reserved for calculation""")
self.dirscf_checkbox.setWhatsThis(
"""Check this box to run the calculation in RAM and avoid hard disk usage for integral storage."""
)
self.gbasis_combox.setWhatsThis(
"""Select from among the standard Gaussian-type basis sets and semi-empirical parameters in GAMESS."""
)
self.checkBox10_3_2.setWhatsThis(
"""Reads the $HESS group from the output file of a previous GAMESS calculation. Only valid for identical molecules."""
)
self.checkBox10_2_2_2.setWhatsThis(
"""Reads the $VEC group from the output of a previous GAMESS calculation. Requires that both the molecule and basis set be identical. Useful for restarted calculations and starting orbitals for electron correlation methods."""
)
self.none_radiobtn.setWhatsThis(
"""Select this button to neglect electron correlation in the calculation."""
)
self.dft_radiobtn.setWhatsThis(
"""Select this button to perform a density functional theory calculation."""
)
self.mp2_radiobtn.setWhatsThis(
"""Select this button to perform a Second-Order Moeller Plesset calculation."""
)
self.dfttyp_combox.setWhatsThis(
"""Select an available density functional in GAMESS.""")
self.gridsize_combox.setWhatsThis(
"""Select the grid spacing for the DFT calculation.""")
self.core_electrons_checkbox.setWhatsThis(
"""Check this box to include both the valence and core electrons in the MP2 calculation."""
)
self.density_conv_combox.setWhatsThis(
"""Selects the accuracy of the electron density convergence for the calculation (CONV)."""
)
self.rmsd_combox.setWhatsThis(
"""Gradient convergence tolerance (OPTTOL), in Hartree/Bohr. Convergence of a geometry search requires the largest component of the gradient to be less than this value, and the root mean square gradient less than 1/3 of OPTTOL. (default=0.0001)"""
)
self.iterations_spinbox.setWhatsThis(
"""Maximum number of SCF iteration cycles (MAXIT).""")
self.edit_input_file_cbox.setWhatsThis(
"""Opens the INP file generated by NanoEngineer-1 in a text editor."""
)
self.whats_this_btn.setWhatsThis("""What's This Help Utility""")
self.run_job_btn.setWhatsThis(
"""Save GAMESS parameters, generates the INP file and launches the GAMESS job."""
)
self.save_btn.setWhatsThis(
"""Save GAMESS parameters and generates the INP file. It does not launch the GAMESS job."""
)
self.cancel_btn.setWhatsThis("""Cancels changes and closes dialog.""")
class GamessProp(QDialog, Ui_GamessPropDialog):
"""
The Gamess Jig Properties dialog used for:
- running a GAMESS energy calculation on a structure (group of atoms).
- running a GAMESS optimization on a structure.
- setting and saving the GAMESS parameters used for an energy calculation or optimization.
"""
def __init__(self):
QDialog.__init__(self)
self.setModal(True)
self.setupUi(self)
self.ecm_btngrp = QButtonGroup()
self.ecm_btngrp.setExclusive(True)
objId = 0
for obj in self.ecm_grpbox.children():
if isinstance(obj, QAbstractButton):
self.ecm_btngrp.addButton(obj)
self.ecm_btngrp.setId(obj, objId)
objId += 1
self.scftyp_btngrp = QButtonGroup()
self.scftyp_btngrp.setExclusive(True)
objId = 0
for obj in self.scftyp_grpbox.children():
if isinstance(obj, QAbstractButton):
self.scftyp_btngrp.addButton(obj)
self.scftyp_btngrp.setId(obj, objId)
objId += 1
self.connect(self.cancel_btn, SIGNAL("clicked()"), self.reject)
self.connect(self.ecm_btngrp, SIGNAL("buttonPressed(int)"),
self.set_ecmethod)
self.connect(self.multi_combox, SIGNAL("activated(int)"),
self.set_multiplicity)
self.connect(self.run_job_btn, SIGNAL("clicked()"), self.run_job)
self.connect(self.save_btn, SIGNAL("clicked()"), self.accept)
self.connect(self.runtyp_combox, SIGNAL("activated(int)"),
self.calculate_changed)
self.connect(self.choose_color_btn, SIGNAL("clicked()"),
self.change_jig_color)
self.connect(self.whats_this_btn, SIGNAL("clicked()"), self.whats_this)
##self.connect(self.new_btn,SIGNAL("clicked()"),self.addServer)
##self.connect(self.exit_btn,SIGNAL("clicked()"),self.close)
##self.connect(self.server_listview,SIGNAL("currentChanged(QListViewItem*)"),self.changeServer)
##self.connect(self.engine_combox,SIGNAL("activated(const QString&)"),self.engineChanged)
##self.connect(self.del_btn,SIGNAL("clicked()"),self.deleteServer)
self.sManager = ServerManager()
self.servers = self.sManager.getServers()
self.server = self.servers[0]
self.name_linedit.setWhatsThis("""Name of the GAMESS jig.""")
self.runtyp_combox.setWhatsThis(
"""Type of calculation, where "Energy" calculates the Energy Minima,and "Optimization" calculates the "Equilibrium Geometry"."""
)
self.comment_linedit.setWhatsThis(
"""Description, also placed in the comment line of the $DATA section of the INP file."""
)
self.choose_color_btn.setWhatsThis("""Change the GAMESS jig color.""")
self.rhf_radiobtn.setWhatsThis(
"""Restricted Hartree-Fock. All electrons are paired and each spatial orbital is doubly occupied. Cannot be used with multiplicities greater than 1."""
)
self.uhf_radiobtn.setWhatsThis(
"""Unrestricted Hartree-Fock. All electrons are unpaired and spatial (spin) orbitals are uniquely defined for each electron. More time consuming, but more accurate, than ROHF. """
)
self.rohf_radiobtn.setWhatsThis(
"""Restricted Open-shell Hartree-Fock. Spin-paired electrons are assigned to doubly-occupied spatial orbitals, while electrons with unpaired spins are provided unique spatial orbitals."""
)
self.icharg_spinbox.setWhatsThis(
"""The total charge of the structure to be treated quantum mechanically (ICHARG)."""
)
self.multi_combox.setWhatsThis(
"""N + 1, where N is the number of unpaired electrons (MULT).""")
self.memory_spinbox.setWhatsThis(
"""System memory reserved for calculation""")
self.dirscf_checkbox.setWhatsThis(
"""Check this box to run the calculation in RAM and avoid hard disk usage for integral storage."""
)
self.gbasis_combox.setWhatsThis(
"""Select from among the standard Gaussian-type basis sets and semi-empirical parameters in GAMESS."""
)
self.checkBox10_3_2.setWhatsThis(
"""Reads the $HESS group from the output file of a previous GAMESS calculation. Only valid for identical molecules."""
)
self.checkBox10_2_2_2.setWhatsThis(
"""Reads the $VEC group from the output of a previous GAMESS calculation. Requires that both the molecule and basis set be identical. Useful for restarted calculations and starting orbitals for electron correlation methods."""
)
self.none_radiobtn.setWhatsThis(
"""Select this button to neglect electron correlation in the calculation."""
)
self.dft_radiobtn.setWhatsThis(
"""Select this button to perform a density functional theory calculation."""
)
self.mp2_radiobtn.setWhatsThis(
"""Select this button to perform a Second-Order Moeller Plesset calculation."""
)
self.dfttyp_combox.setWhatsThis(
"""Select an available density functional in GAMESS.""")
self.gridsize_combox.setWhatsThis(
"""Select the grid spacing for the DFT calculation.""")
self.core_electrons_checkbox.setWhatsThis(
"""Check this box to include both the valence and core electrons in the MP2 calculation."""
)
self.density_conv_combox.setWhatsThis(
"""Selects the accuracy of the electron density convergence for the calculation (CONV)."""
)
self.rmsd_combox.setWhatsThis(
"""Gradient convergence tolerance (OPTTOL), in Hartree/Bohr. Convergence of a geometry search requires the largest component of the gradient to be less than this value, and the root mean square gradient less than 1/3 of OPTTOL. (default=0.0001)"""
)
self.iterations_spinbox.setWhatsThis(
"""Maximum number of SCF iteration cycles (MAXIT).""")
self.edit_input_file_cbox.setWhatsThis(
"""Opens the INP file generated by NanoEngineer-1 in a text editor."""
)
self.whats_this_btn.setWhatsThis("""What's This Help Utility""")
self.run_job_btn.setWhatsThis(
"""Save GAMESS parameters, generates the INP file and launches the GAMESS job."""
)
self.save_btn.setWhatsThis(
"""Save GAMESS parameters and generates the INP file. It does not launch the GAMESS job."""
)
self.cancel_btn.setWhatsThis("""Cancels changes and closes dialog.""")
def showDialog(self, job):
"""
Display the GAMESS Jig Properties dialog
"""
self.gamessJig = job.gamessJig
self.job = job
self.pset = self.gamessJig.pset
self.win = self.gamessJig.assy.w
self.glpane = self.gamessJig.assy.o
if self._setup(): return
self.exec_()
######Private or helper methods###############################
def _setup(self):
"""
Setup widgets to initial (default or defined) values. Return True on error.
"""
#To fix bug 684
#if gamess.is_disabled():
# self.run_job_btn.setEnabled(False)
#else:
# self.run_job_btn.setEnabled(True)
self.jig_attrs = self.gamessJig.copyable_attrs_dict(
) # Save the jig's attributes in case of Cancel.
# Jig color
self.original_normcolor = self.gamessJig.normcolor
self.jig_QColor = RGBf_to_QColor(
self.gamessJig.normcolor) # Used as default color by Color Chooser
self.jig_color_pixmap = get_widget_with_color_palette(
self.jig_color_pixmap, self.jig_QColor)
# Init the top widgets (name, runtyp drop box, comment)
self.name_linedit.setText(self.gamessJig.name)
self.runtyp_combox.setCurrentIndex(self.pset.ui.runtyp) # RUNTYP
self.calculate_changed(self.pset.ui.runtyp)
self.comment_linedit.setText(self.pset.ui.comment)
# Electronic Structure Properties section.
btn = self.scftyp_btngrp.button(
self.pset.ui.scftyp) # RHF, UHF, or ROHF
btn.setChecked(True)
self.icharg_spinbox.setValue(self.pset.ui.icharg) # Charge
self.multi_combox.setCurrentIndex(self.pset.ui.mult) # Multiplicity
# Disable RHF if multiplicity is not the first item.
if self.pset.ui.mult == 0:
self.rhf_radiobtn.setEnabled(1) # Enable RHF
else:
self.rhf_radiobtn.setEnabled(0) # Disable RHF
# System Memory and Usage
self.dirscf_checkbox.setChecked(self.pset.ui.dirscf) # DIRSCF
self.memory_spinbox.setValue(self.pset.ui.memory) # Memory
# Electron Correlation Method and Basis Set
ecm = self.pset.ui.ecm
btn = self.ecm_btngrp.button(self.pset.ui.ecm) # None, DFT or MP2
btn.setChecked(True)
self.set_ecmethod(self.pset.ui.ecm) # None, DFT or MP2
self.gbasis_combox.setCurrentIndex(self.pset.ui.gbasis) # Basis set
# Load the combo box with all the valid DFT functions.
self._load_dfttyp_combox()
self.dfttyp_combox.setCurrentIndex(
self.pset.ui.dfttyp) # DFT Functional
self.gridsize_combox.setCurrentIndex(
self.pset.ui.gridsize) # Grid Size
self.core_electrons_checkbox.setChecked(
self.pset.ui.ncore) # Include core electrons
# Convergence Criteria
self.density_conv_combox.setCurrentIndex(
self.pset.ui.conv) # Density Convergence
self.rmsd_combox.setCurrentIndex(
self.pset.ui.rmsdconv) # RMSD Convergence
self.iterations_spinbox.setValue(self.pset.ui.iterations) # Iterations
# These have been removed per discussions with Damian.
# Mark 050628
# self.extrap_checkbox.setChecked(self.pset.ui.extrap) # EXTRAP
# self.damp_checkbox.setChecked(self.pset.ui.damp) # DAMP
# self.diis_checkbox.setChecked(self.pset.ui.diis) # DIIS
# self.shift_checkbox.setChecked(self.pset.ui.shift) # SHIFT
# self.soscf_checkbox.setChecked(self.pset.ui.soscf) # SOSCF
# self.rstrct_checkbox.setChecked(self.pset.ui.rstrct) # RSTRCT
# Load the server combo box
#self._reloadServerList() # Not used in A6. Mark.
# If there is an error, return 1. NIY.
return 0
def _reloadServerList(self):
"""
Load the server combo box
"""
self.server_combox.clear()
for s in self.servers:
self.server_combox.insertItem(100, s.hostname + "-" + s.engine)
# 100 makes sure item is appended to list. [mark 2007-05-04]
if self.server not in self.servers:
self.server = self.servers[0]
indx = self.servers.index(self.server)
self.server_combox.setCurrentIndex(indx)
def _load_dfttyp_combox(self):
"""
Load list of DFT function in a combobox widget
"""
self.dfttyp_combox.clear() # Clear all combo box items
if self.server.engine == 'GAMESS':
for f in gms_dfttyp_items:
self.dfttyp_combox.insertItem(100, f)
# 100 makes sure item is appended to list. [mark 2007-05-04]
elif self.server.engine == 'PC GAMESS':
for f in pcgms_dfttyp_items:
self.dfttyp_combox.insertItem(100, f)
# 100 makes sure item is appended to list. [mark 2007-05-04]
else:
print "load_dfttyp_combox: Unknown GAMESS Version. Loading GAMES DFT functionals."
for f in gms_dfttyp_items:
self.dfttyp_combox.insertItem(100, f)
# 100 makes sure item is appended to list. [mark 2007-05-04]
def _update_gbasis_list(self, val):
"""
Add/remove AM1 and PM3 to/from the gbasis list.
"""
citem = self.gbasis_combox.currentIndex()
if val == DFT or val == MP2:
if self.gbasis_combox.count() == 18:
self.gbasis_combox.removeItem(0)
self.gbasis_combox.removeItem(0)
self.gbasis_combox.setCurrentIndex(max(0, citem - 2))
else:
if self.gbasis_combox.count() != 18:
self.gbasis_combox.insertItem(
0, "PM3") # 0 prepends item to list.
self.gbasis_combox.insertItem(0, "AM1")
self.gbasis_combox.setCurrentIndex(citem + 2)
def _save_ui_settings(self):
"""
Save the UI settings in the Gamess jig pset.
There is one setting for each pset.
"""
self.pset.ui.comment = str(self.comment_linedit.text()) # Description
self.pset.ui.runtyp = self.runtyp_combox.currentIndex(
) # RUNTYP = Energy or Optimize
# Electronic Structure Props and Basis Set section.
self.pset.ui.scftyp = self.scftyp_btngrp.checkedId(
) # SCFTYP = RHF, UHF, or ROHF
self.pset.ui.icharg = self.icharg_spinbox.value() # Charge
self.pset.ui.mult = self.multi_combox.currentIndex() # Multiplicity
# System Memory and Usage
self.pset.ui.memory = self.memory_spinbox.value() # Memory
self.pset.ui.dirscf = self.dirscf_checkbox.isChecked() # DIRSCF
# Electron Correlation Method
self.pset.ui.ecm = self.ecm_btngrp.checkedId() # None, DFT or MP2
#self.pset.ui.inttyp = self.ecm_btngrp.selectedId() # INTTYP
self.pset.ui.gbasis = self.gbasis_combox.currentIndex() # Basis Set
self.pset.ui.gbasisname = str(self.gbasis_combox.currentText())
self.pset.ui.dfttyp = self.dfttyp_combox.currentIndex(
) # DFT Functional Type
self.pset.ui.gridsize = self.gridsize_combox.currentIndex(
) # Grid Size
self.pset.ui.ncore = self.core_electrons_checkbox.isChecked(
) # Include core electrons
# Convergence Criteria
self.pset.ui.conv = self.density_conv_combox.currentIndex(
) # Density Convergence
self.pset.ui.rmsdconv = self.rmsd_combox.currentIndex(
) # RMSD Convergence
self.pset.ui.iterations = self.iterations_spinbox.value() # Iterations
# self.pset.ui.extrap = self.extrap_checkbox.isChecked() # EXTRAP
# self.pset.ui.damp = self.damp_checkbox.isChecked() # DAMP
# self.pset.ui.diis = self.diis_checkbox.isChecked() # DIIS
# self.pset.ui.shift = self.shift_checkbox.isChecked() # SHIFT
# self.pset.ui.soscf = self.soscf_checkbox.isChecked() # SOSCF
# self.pset.ui.rstrct = self.rstrct_checkbox.isChecked() # RSTRCT
def _save_job_parms(self):
calculate = ['Energy', 'Optimization']
self.job.Calculation = calculate[self.pset.ui.runtyp]
self.job.Description = self.pset.ui.comment
self.job.server = self.server
##Copy some attributes from the server object to job description
self.job.Server_id = self.server.server_id
self.job.Engine = self.server.engine
######End of private or helper methods.########################
###### Unused methods ###############
def openServerManager(self):
"""
Pop up ServerManagerDialog to edit the properties of the servers.
"""
self.sManager.showDialog(self.server)
self.servers = self.sManager.getServers()
self._reloadServerList()
def serverChanged(self, si):
"""
User has changed server, so update the DFT comboBox. Currently not used.
"""
self.server = self.servers[si]
self._load_dfttyp_combox()
###### End of unused methods ###############
##########Slot methods for some GUI controls################
def calculate_changed(self, val):
"""
"""
if val == 0: # Energy
self.rmsd_lbl.setEnabled(0)
self.rmsd_combox.setEnabled(0)
self.iterations_lbl.setEnabled(0)
self.iterations_spinbox.setEnabled(0)
# self.extrap_checkbox.setEnabled(0)
# self.rstrct_checkbox.setEnabled(0)
# self.damp_checkbox.setEnabled(0)
# self.diis_checkbox.setEnabled(0)
# self.shift_checkbox.setEnabled(0)
# self.soscf_checkbox.setEnabled(0)
else: # Optimization
self.rmsd_lbl.setEnabled(1)
self.rmsd_combox.setEnabled(1)
self.iterations_lbl.setEnabled(1)
self.iterations_spinbox.setEnabled(1)
# self.extrap_checkbox.setEnabled(1)
# self.rstrct_checkbox.setEnabled(1)
# self.damp_checkbox.setEnabled(1)
# self.diis_checkbox.setEnabled(1)
# self.shift_checkbox.setEnabled(1)
# self.soscf_checkbox.setEnabled(1)
def set_multiplicity(self, val):
"""
Enable/disable widgets when user changes Multiplicity.
"""
if val != 0:
qt4todo("if scftyp[self.scftyp_btngrp.selectedId()] != 'RHF':")
#if scftyp[self.scftyp_btngrp.selectedId()] != 'RHF':
# self.rhf_radiobtn.setEnabled(0)
# return
ret = QMessageBox.warning(
self, "Multiplicity Conflict",
"If Multiplicity is greater than 1, then <b>UHF</b> or <b>ROHF</b> must be selected.\n"
"Select Cancel to keep <b>RHF</b>.", "&UHF", "&ROHF", "Cancel",
0, 2)
if ret == 0: # UHF
self.uhf_radiobtn.toggle()
self.rhf_radiobtn.setEnabled(0)
elif ret == 1: # ROHF
self.rohf_radiobtn.toggle()
self.rhf_radiobtn.setEnabled(0)
elif ret == 2: # Cancel
self.multi_combox.setCurrentIndex(0)
elif val == 0:
self.rhf_radiobtn.setEnabled(1)
def set_ecmethod(self, val):
"""
Enable/disable widgets when user changes Electron Correlation Method.
"""
#print "set_ecmethod = ", val
if val == DFT:
self.dfttyp_label.setEnabled(1)
self.dfttyp_combox.setEnabled(1)
self.gridsize_label.setEnabled(1)
self.gridsize_combox.setEnabled(1)
self.core_electrons_checkbox.setChecked(0)
self.core_electrons_checkbox.setEnabled(0)
elif val == MP2:
self.core_electrons_checkbox.setEnabled(1)
self.dfttyp_label.setEnabled(0)
self.dfttyp_combox.setEnabled(0)
self.gridsize_label.setEnabled(0)
self.gridsize_combox.setEnabled(0)
else: # None = Hartree-Fock
self.dfttyp_label.setEnabled(0)
self.dfttyp_combox.setEnabled(0)
self.gridsize_label.setEnabled(0)
self.gridsize_combox.setEnabled(0)
self.core_electrons_checkbox.setChecked(0)
self.core_electrons_checkbox.setEnabled(0)
# AM1 and PM3 are not options for DFT or MP2.
# We have to remove or add them from the combo box.
self._update_gbasis_list(val)
def open_tmp_inputfile(self):
"""
Writes a temporary GAMESS inputfile of the current Gamess jig and opens the
file in an editor.
"""
# Make tmp_inputfile filename (i.e. ~/Nanorex/temp/jigname_parms_info.inp)
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
tmpdir = find_or_make_Nanorex_subdir('temp')
basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info(
'_')
tmp_inputfile = os.path.join(tmpdir, "%s.inp" % basename)
# Write INP file (in ~/Nanorex/temp subdirectory)
from analysis.GAMESS.files_gms import writegms_inpfile
writegms_inpfile(tmp_inputfile, self.gamessJig)
from platform_dependent.PlatformDependent import open_file_in_editor
open_file_in_editor(tmp_inputfile)
def run_job(self):
"""
Slot method for the 'Save and Run' button
"""
self.accept()
# Run GAMESS job. Return value r:
# 0 = success
# 1 = job cancelled
# 2 = job failed.
r = self.job.launch()
if r == 1: # Job was cancelled
env.history.message(redmsg("GAMESS job cancelled."))
return
if r == 2: # Job failed.
env.history.message(
redmsg(
"GAMESS job failed. Maybe you didn't set the right Gamess executable file. Make sure you can run the same job manually."
))
return
# Job success.
fn = self.gamessJig.outputfile
# Print energy or move atoms
if self.pset.ui.runtyp == 0: #Energy
self.gamessJig.print_energy()
else: # Optimize
try:
r = self.gamessJig.move_optimized_atoms()
# r = insertgms(self.gamessJig.assy, fn)
except:
print_compact_traceback(
"GamessProp.run_job(): error reading GAMESS OUT file [%s]: "
% fn)
env.history.message(
redmsg("Internal error while inserting GAMESS geometry: " +
fn))
else:
if r:
env.history.message(redmsg("Atoms not adjusted."))
else:
self.gamessJig.assy.changed(
) # The file and the part are not the same.
self.gamessJig.print_energy(
) # Print the final energy from the optimize OUT file, too.
env.history.message("Atoms adjusted.")
def change_jig_color(self):
"""
Slot method to change the jig's color.
"""
color = QColorDialog.getColor(self.jig_QColor, self)
if color.isValid():
self.jig_QColor = color
self.jig_color_pixmap = get_widget_with_color_palette(
self.jig_color_pixmap, self.jig_QColor)
self.gamessJig.color = self.gamessJig.normcolor = QColor_to_RGBf(
color)
self.glpane.gl_update()
def accept(self):
"""
The slot method for the 'Save' button.
"""
QDialog.accept(self)
self.gamessJig.try_rename(self.name_linedit.text())
self._save_ui_settings()
self.gamessJig.update_gamess_parms(
) # Update all the GAMESS parameters.
self._save_job_parms()
if self.edit_input_file_cbox.isChecked():
self.open_tmp_inputfile()
def reject(self):
"""
The slot method for the 'Cancel' button.
"""
QDialog.reject(self)
self.gamessJig.attr_update(
self.jig_attrs) # Restore attributes of the jig.
# self.gamessJig.color = self.gamessJig.normcolor = self.original_normcolor
self.gamessJig.cancelled = True
self.glpane.gl_update()
def whats_this(self):
from PyQt4.Qt import QWhatsThis, QDialog
QWhatsThis.enterWhatsThisMode()
