subroutines for polarizable model

Examples/BK3.dat

@@ -0,0 +1,10 @@
+1
+298.0 0.0
+O1    1.000000   1.00000    0.000   !oxygen
+DM    1.162874   1.21043    0.000   !virtual site
+G1    1.162874   1.21043    0.000   !drude particle attached to the virtual site
+H2    1.975000   1.00000    0.000   !hydrogen 1
+G2    1.975000   1.00000    0.000   !drude particle attached to hydrogen 1
+H3    0.755550   1.94386    0.000   !hydrogen 2
+G3    0.755550   1.94386    0.000   !drude particle attached to hydogen 2
+

Examples/BK3.mcf

@@ -0,0 +1,73 @@
+!********************************************************************************
+!   Cassandra - An open source atomistic Monte Carlo software package
+!   developed at the University of Notre Dame.
+!   http://cassandra.nd.edu
+!   Prof. Edward Maginn <ed@nd.edu>
+!   Copyright (2013) University of Notre Dame du Lac
+!
+!   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 3 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, see <http://www.gnu.org/licenses/>.
+!********************************************************************************
+!*******************************************************************************
+!
+! This is an input file for water BK3
+!
+! Force field - BK3
+! J. Chem. Phys. 2013, 138, 204507
+!*******************************************************************************
+
+!**********************************************************************************
+!
+!**********************************************************************************
+
+!    type  element mass    charge    Exp-6 A (Kelvin)  B (A^-1)  C (Kelvin)  rmin  sigma alpha
+# Atom_Info
+7
+1    O1    O    16.00      0.0000    Born  38727700.7  3.56      399304.244  0.87  1.0   0.0
+2    DM    D    0.000      0.0000    Born  0.000000    0.01      0.0         1.0   1.0   0.0
+3    G1    G    0.000      -1.168    Born  0.0         0.01      0.0         1.0   0.71  0.72
+4    H2    H    1.000      0.0000    Born  0.0         0.01      0.0         1.0   1.00  0.0
+5    G2    G    0.000      0.584     Born  0.0         0.01      0.0         1.0   0.40  0.36
+6    H3    H    1.000      0.0000    Born  0.0         0.01      0.0         1.0   1.00  0.0
+7    G3    G    0.000      0.584     Born  0.0         0.01      0.0         1.0   0.40  0.36
+
+
+# Bond_Info
+6
+1    1    2    fixed     0.2661
+2    2    3    harmonic  131621.3 0.000  !0.5*spring constant for the drude particle (K = q*q/alpha), equilibrium bond length l=0 (shell rests on core)
+3    1    4    fixed     0.9750
+4    1    6    fixed     0.9750
+5    4    5    harmonic  65810.64 0.000  
+6    6    7    harmonic  65810.64 0.000
+
+# Angle_Info
+3
+1    4    1    6   fixed  104.52
+2    2    1    4   fixed   52.26
+3    2    1    6   fixed   52.26
+
+# Dihedral_Info
+0
+
+# Fragment_Info
+1
+1  7  1 2 3 4 5 6 7
+
+# Improper_Info
+0
+
+# Fragment_Connectivity
+0
+
+END

Examples/BK3_Cl.dat

@@ -0,0 +1,4 @@
+1
+298.0 0.0
+Cl    1.00   2.00    0.000 !Chloride (core)
+G1    1.00   2.00    0.000 !drude particle (shell)

Examples/BK3_Na.dat

@@ -0,0 +1,6 @@
+1
+298.0 0.0
+Na    1.50   1.20    0.000  !Na atom (core)
+G1    1.50   1.20    0.000  !drude particle (shell)
+
+

Examples/Cl_BK3.mcf

@@ -0,0 +1,59 @@
+!********************************************************************************
+!   Cassandra - An open source atomistic Monte Carlo software package
+!   developed at the University of Notre Dame.
+!   http://cassandra.nd.edu
+!   Prof. Edward Maginn <ed@nd.edu>
+!   Copyright (2013) University of Notre Dame du Lac
+!
+!   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 3 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, see <http://www.gnu.org/licenses/>.
+!********************************************************************************
+!*******************************************************************************
+!
+! This is an input file for BK3 Cl.
+!
+
+!*******************************************************************************
+
+!**********************************************************************************
+!Molecular connectivity file for water.pdb
+!**********************************************************************************
+
+
+# Atom_Info
+2
+1    Cl  Cl    35.45  -11.0  Born 113056021.0 3.10  962178.90  0.788  0.96 0.0
+2    G1   G    0.000   10.0  Born         0.0 0.01        0.0  1.000  0.96 3.5
+
+
+# Bond_Info
+1
+1 1 2 harmonic 1984745.7 0.0
+
+# Angle_Info
+0
+
+# Dihedral_Info
+0
+
+# Fragment_Info
+1
+1 2 1 2
+
+# Improper_Info
+0
+
+# Fragment_Connectivity
+0
+
+END

Examples/H2O_NaCl_GEMC.inp

@@ -0,0 +1,151 @@
+!******************************************************************************
+!
+! This is an input file for SPC/E water.
+!
+! Created by Eliseo Marin 12/13/13
+!*******************************************************************************
+
+
+# Run_Name
+BK3_salt_H2O_GEMC
+!--------------
+
+# Sim_Type
+GEMC
+!---------------
+
+# Nbr_Species
+3
+!----------------
+
+# VDW_Style
+Born cut_tail 12.0   !Born (bukcingham potential) cut-off distance 12.0 A
+Born cut_tail 19.0
+!----------------
+
+# Rcutoff_Low
+0.1
+!----------------
+
+# Mixing_Rule
+kong                ! Kong mixing rule for buckingham potential
+!----------------
+
+# Charge_Style
+coul Gaussian_charge 12.00 0.0001    !Ewald sum for Gaussian charge
+coul Gaussian_charge 19.00 0.0001
+!----------------
+
+# Intra_Scaling
+0.0  0.0  0.0  0.0
+0.0  0.0  0.0  0.0
+0.0  0.0  0.0  0.0
+0.0  0.0  0.0  0.0
+0.0  0.0  0.0  0.0
+0.0  0.0  0.0  0.0
+!------------------
+
+# Molecule_Files
+BK3.mcf    256
+Na_BK3.mcf 2
+Cl_BK3.mcf 2
+!---------------------
+
+# Pair_Energy
+FALSE                     !Pair_Energy must be set to FALSE
+
+# Box_Info
+2
+CUBIC
+30.0
+
+CUBIC
+40.0
+
+# Temperature_Info
+473.15 473.15
+!------------------
+
+# Seed_Info
+2082012 82012
+!-------------------
+
+# Move_Probability_Info
+
+# Prob_Translation
+0.25
+0.002 0.002 0.002      !adjustable parameter for multiparticle translation move
+0.002 0.002 0.002
+
+# Prob_Rotation
+0.25
+0.001 0.001 0.001      !adjustable parameter for multiparticle rotation move
+0.001 0.001 0.001
+
+# Prob_Volume
+0.1
+300
+300
+
+# Prob_Swap
+0.4
+insertion method
+reservior
+insertion method
+none
+insertion method
+none
+# Prob_Species_Swap
+1.0 1.0 1.0
+
+# Done_Probability_Info
+
+!----------------------
+# Bond_Prob_Cutoff
+1.0E-10
+
+# CBMC_Info
+kappa_ins 10
+kappa_rot 0
+kappa_dih 10
+rcut_cbmc 9.0 9.0
+
+# Start_Type
+make_config
+250 6
+2   0
+2   0
+
+# Run_Type
+Equilibration   100 100
+!------------------
+
+# Average_Info ( 0 == yes, 1 = No)
+1
+
+# Frequency_Info
+freq_type    none
+Nthermofreq  100
+Ncoordfreq   1000
+MCsteps      1000
+# Done_Frequency_Info
+!--------------------
+
+# Property_Info 1 
+Energy_Total
+Volume
+Nmols
+
+# Property_Info 2 
+Energy_Total
+Volume
+Nmols
+Pressure1            !Calculation of pressure by performing a (positive) trial volume change
+Pressure2            !Calculation of pressure by performing a (negative) trial volume change (without evaluation of virial pressure)
+
+# Fragment_Files
+BK3.dat 1
+BK3_Na.dat 2
+BK3_Cl.dat 3
+
+END