qmmm.py

########################################################################
#                                                                      #
# This module contains all of the qmmm namelist variables for the      #
# amber programs and automatically loads those dictionaries with the   #
# default values found in that program (sander only).                  #
#                                                                      #
#          Last updated: 01/03/2011                                    #
#                                                                      #
########################################################################

########################## GPL LICENSE INFO ############################

#  Copyright (C) 2010  Jason Swails and Ben Roberts

#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.

#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
   
#  You should have received a copy of the GNU General Public License
#  along with this program; if not, write to the Free Software
#  Foundation, Inc., 59 Temple Place - Suite 330,
#  Boston, MA 02111-1307, USA.

# All of the variables in the pb namelist
class qmmm:

   def __init__(self):
      self.sander = { 'qmcut' : -1,'iqmatoms' : '','qmmask' : '','qmgb' : 2,'qm_theory' : '',
                      'qmcharge' : 0,'qmqmdx' : 1,'verbosity' : 0,'tight_p_conv' : 0,'scfconv' : 1.0e-8,
                      'errconv' : 1e-1,'ndiis_matrices' : 6,'ndiis_attempts' : 0,'printcharges' : 0,
                      'printdipole' : 0,'peptide_corr' : 0,'itrmax' : 1000,'qmshake' : 1,'qmqm_erep_incore' : 1,
                      'qmmmrij_incore' : 1,'lnk_dis' : 1.09,'lnk_atomic_no' : 1,'lnk_method' : 1,'spin' : 1,
                      'pseudo_diag' : 1,'pseudo_diag_criteria' : 0.05,'qm_ewald' : 1,'qm_pme' : 1,'kmaxqx' : 5,
                      'kmaxqy' : 5,'kmaxqz' : 5,'ksqmaxq' : 27,'writepdb' : 0,'qmmm_int' : 1,'adjust_q' : 2,
                      'diag_routine' : 1, 'density_predict' : 0,'fock_predict' : 0, 
                      'fockp_d1' : 2.4,'fockp_d2' : -1.2,'fockp_d3' : -0.8,'fockp_d4' : 0.6,'idc' : 0,'divpb' : 0, 
                      'dftb_maxiter' : 70,'dftb_disper' : 0,'dftb_3rd_order' : 'NONE','dftb_chg' : 0, 
                      'dftb_telec' : 0,'dftb_telec_step' : 0,'qmmm_omp_max_threads' : 1, 
                      'chg_lambda' : 1,'nearest_qm_solvent' : 0,'nearest_qm_solvent_fq' : 1, 
                      'nearest_qm_solvent_resname' : 'WAT '}