path: root/cad/src/analysis/GAMESS/GamessProp.py

# Copyright 2005-2009 Nanorex, Inc.  See LICENSE file for details.
"""
GamessProp.py

@author: Mark
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc.  See LICENSE file for details.
"""

import os

from PyQt4.Qt import QDialog
from PyQt4.Qt import QButtonGroup
from PyQt4.Qt import QAbstractButton
from PyQt4.Qt import SIGNAL
from PyQt4.Qt import QMessageBox
from PyQt4.Qt import QColorDialog

import foundation.env as env

from analysis.GAMESS.GamessPropDialog import Ui_GamessPropDialog
from processes.ServerManager import ServerManager
from utilities.Log import redmsg
##from files_gms import insertgms
from utilities.debug import print_compact_traceback
from widgets.widget_helpers import RGBf_to_QColor, QColor_to_RGBf, get_widget_with_color_palette
from utilities.qt4transition import qt4todo


# Ask Bruce where all this should ultimately live.

# This is the GAMESS UI widget default settings (for energy).

ui={'comment':'','runtyp':0,'scftyp':0, 'icharg':0, 'mult':0, 'gbasis':0, 'ecm':0, 'dfttyp':0, 'gridsize':1, 'ncore':0,
        'conv':1, 'rmsdconv':1, 'iterations':50, 'memory':70, 'extrap':1, 'dirscf':1, 'damp':0, 'shift':0, 'diis':0,'soscf':0,'rstrct':0,
        'gbasisname':'AM1'}

# These are the GAMESS parms set defaults (for energy).

# $CONTRL group section ####################################
#
# The general form for the $CONTRL group is (keyword order does not matter):
#
#   $CONTRL
#   runtyp=energy coord=unique scftyp=rhf icharg=1 mult=1 mplevl=0
#   maxit=200 inttyp=pople icut=11 qmttol=1.0E-6
#   $END
#
# $CONTRL group keywords and their default values.
contrl={'runtyp':'energy', 'coord':'unique', 'scftyp':'RHF', 'icharg':0, 'mult':1, 'mplevl':'0',
        'maxit':50, 'icut':11, 'inttyp':'hondo', 'qmttol':'1.0E-6', 'dfttyp':0, 'nprint':9}
# Note: The 'dfttyp' keyword in the $CONTRL group is only valid for PC GAMESS.

# $CONTRL keywords and their optional values
runtyp=['energy', 'optimize'] # RUNTYP
scftyp=['RHF', 'UHF', 'ROHF'] # SCFTYP
mplevl=[ 0, 0, '2'] # MPLEVL: None=0, DFT=0, MP2='2'
inttyp=['pople', 'pople', 'hondo'] # Set by EMC, None=POPLE, DFT=POPLE, MP2=HONDO
nprint=-5,-2,7,8,9 # Not currently used. nprint is always 9 for now.

# $SCF group section ####################################
#
# The general form for the $SCF group is (keyword order does not matter):
#
#   $SCF
#   conv=10E-05 coord=unique extrap=.T. dirscf=.T. damp=.F shift=.F. diis=.T. soscf=.F. rstrct=.F.
#   $END
#
# $SCF group keywords and their default values.
scf={'conv':1, 'nconv':1, 'extrap':'.T.','dirscf':'.T.', 'damp':'.F.', 'shift':'.F.', 'diis':'.T.',
     'soscf':'.F.','rstrct':'.F.'}
# Note: Keyword 'conv' is used by GAMESS, 'nconv' is used by PC GAMESS.

# CONV keyword and its optional values
conv='10E-04','10E-05','10E-06','10E-07' # Density Convergence

# Useful true or false tuple.
tf='.F.', '.T.' # True/False for SCF parameters

# $SYSTEM group section ####################################
#
# The general form for the $SYSTEM group is:
#
#   $SYSTEM
#   timlim=1000 memory=70000000
#   $END
#
# $SYSTEM group keywords and their default values.
system={'timlim':1000, 'memory':70000000}

# $MP2 group section ####################################
#
# The general form for the $MP2 group is (keyword order does not matter):
#
#   $MP2
#   ncore=0
#   $END
#
# The $MP2 group is written only when the Electron Correlation Method = MP2.
# To include core electrons, we add the keyword NCORE=0.
# To exclude core electrons, we leave NCORE out of the $MP2 group altogether.
# So, with the checkbox not checked, ncore=0, and the NCORE keyword isn't written.
# With the checkbox checked, ncore='0' (string type), NCORE=0 is written.  Mark 050528.
mp2={'ncore':0} # Core electrons for MP2
ncore=[0, '0'] # Core electrons: Not included=0, Included='0'.

# Useful Electron Correlation Method variables.
ecm=['None', 'DFT', 'MP2']
DFT=1
MP2=2

# $DFT group section (GAMESS only) ##############################
#
# The general form for the $DFT group is (keyword order does not matter):
#
#   $DFT
#    dfttyp=SLATER nrad=96 nthe=12 nphi=24 switch=3.0E-04
#   $END
#
# $DFT group keywords and their default values.
dft={'dfttyp':0, 'nrad':0}
# Note: In PC GAMESS, the $DFT group contains the grid size parameters
# only, and the DFTTYP keyword is placed in the $CONTRL group.

# DFTTYP functions for GAMESS, specified by the DFTTYP keyword in the $DFT group.
# The PC GAMESS DFTTYP functions are different (see pcgms_dfttyp_items).
# The DFTTYP keyword values are the same without the '(x)' text.  The selected
# item is written to the $DFT group like this: dfttyp=SLATER
gms_dfttyp_items='SLATER (E)','BECKE (E)','GILL (E)','PBE (E)','VWN (C)', \
    'LYP (C)', 'OP (C)', 'SVWN (E+C)', 'SLYP (E+C)', 'SOP (E+C)', 'BVWN (E+C)', \
    'BLYP (E+C)', 'BOP (E+C)', 'GVWN (E+C)', 'GLYP (E+C)', 'GOP (E+C)', \
    'PBEVWN (E+C)', 'PBELYP (E+C)', 'PBEOP (E+C)', 'BHHLYP (H)', 'B3LYP (H)'

# DFTTYP functions for PC GAMESS. These are different for GAMESS.
# The DFTTYP keyword values are the same without the '(x)' text.
pcgms_dfttyp_items = 'SLATER (E)','B88 (E)','GILL96 (E)','XPBE96 (E)','LYP (C)', \
    'VWN1RPA (C)','VWN5 (C)','PW91LDA (C)','CPBE96 (C)','CPW91 (C)', \
    'SLYP (E+C)','BLYP (E+C)','GLYP (E+C)','SVWN1RPA (E+C)', \
    'BVWN1RPA (E+C)','VWN5 (E+C)','BVWN5 (E+C)','PBE96 (E+C)', \
    'PBEPW91 (E+C)','B3LYP1 (H)','BELYP5 (H)','BHHLYP (H)','PBE0 (H)', \
    'PBE1PW91 (H)','B3PW91 (H)'

# The 5 DFT grid size parameters for:
#   - Course
#   - Default,
#   - Fine
#   - Very Fine
#   - Army Grade.
# These are the $DFT grid size parameters for GAMESS.
gms_gridsize= '=48 nthe=12 nphi=24 switch=1.0E-03', \
                '96 nthe=12 nphi=24 switch=3.0E-04', \
                '96 nthe=24 nphi=48 switch=3.0E-04', \
                '96 nthe=36 nphi=72 switch=3.0E-04', \
                '96 nthe=36 nphi=72 switch=3.0E-04'
# Note: the first number is the 'nrad' parm. 'nrad=' is printed by the prin1 method.
# Also, Damian needs to supply parameters for "Very Fine" (Army Grade used twice).

# These are the $DFT grid size parameters for PC GAMESS.
pcgms_gridsize='48 lmax=19', \
                            '63 lmax=29', \
                            '63 lmax=53', \
                            '95 lmax=89', \
                            '128 lmax=131'
# Note: the first number is the 'nrad' parm. 'nrad=' is printed by the prin1 method.

# $GUESS group section ##############################
#
# The general form for the $GUESS group is:
#
#   $GUESS
#    guess=huckel
#   $END
#
# $GUESS group keywords and their default values.
guess={'guess':'huckel'}

# The GUESS keyword and its optional values
guess_keyword=['huckel', 'moread']
# Note: Writing the 'guess' keyword requires special case code in the prin1 method
# since its group name is the same ('guess'). Mark 050529

# $STATPT group section ##############################
#
# The general form for the $STATPT group is:
#
#   $STATPT
#    hess=guess
#   $END
#
# $STATPT group keywords and their default values.
statpt={'hess':'guess', 'opttol':1}

# The HESS keyword and its optional values
hess=['guess', 'read']

# OPTTOL keyword and its optional values
opttol=[0.0001, 0.00001, 0.000001, 0.0000001] # RMSD Convergence

# $BASIS group section ##############################
#
# The general form for the $BASIS group is:
#
#   $BASIS
#   gbasis=AM1 NGAUSS=0 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.
#   $END
#
# $BASIS group keywords and their default values.
basis={'gbasis':'AM1'}

# The GBASIS keyword and its optional values
gbasis='AM1 NGAUSS=0 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'PM3 NGAUSS=0 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'STO NGAUSS=3 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'STO NGAUSS=6 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N21 NGAUSS=3 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N21 NGAUSS=3 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N31 NGAUSS=6 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N31 NGAUSS=6 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N31 NGAUSS=6 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.T. DIFFS=.F.', \
    'N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 NFFUNC=0 DIFFSP=.T. DIFFS=.F.', \
    'N31 NGAUSS=6 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.T. DIFFS=.T.', \
    'N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 NFFUNC=0 DIFFSP=.T. DIFFS=.T.', \
    'N311 NGAUSS=6 NDFUNC=0 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N311 NGAUSS=6 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 NFFUNC=0 DIFFSP=.F. DIFFS=.F.', \
    'N311 NGAUSS=6 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.T. DIFFS=.F.', \
    'N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 NFFUNC=0 DIFFSP=.T. DIFFS=.F.', \
    'N311 NGAUSS=6 NDFUNC=1 NPFUNC=0 NFFUNC=0 DIFFSP=.T. DIFFS=.T.', \
    'N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 NFFUNC=0 DIFFSP=.T. DIFFS=.T.'


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()