#chemdb_queue_nwchem - version 1.0

#########################  START NWCHEM INPUT DECK - NWJOB 266022 ########################
#
# queue_nwchem_JobId: 5e0f8f2049db98ed7620ac1a
# queue_nwchem_restart_count: 0
#
echo
#nwchem_input  C1H4Pt27-aimdmm.nw
#nwchem_output C1H4Pt27-aimdmm.out00
#nwchem_done   C1H4Pt27-aimdmm.done
#
#mformula_off
#
#transfer_files *.nw *.xyz *.ion_motion *.emotion *.fei *.cif *.hist *.gr *.dat *.meta_gaussians *.cube
#bad_files md_xs
#
#curdir we31869.emsl.pnl.gov:/media/seagate2/Projects/Other/C1H4Pt27-aimdmm
#
#permdir C1H4Pt27-aimdmm
#deletescratch no
#queuesave no
#
#machine eric-test
#cputime 8:05:00
#ncpus 32
#queue regular
#
#mformula = C1H4Pt27

######################
# AIMD-MM Simulation #
######################

#Molarity = 1.000
#ASA = 665.5 angstrom squared.
#SAV = 549.8 angstrom cubed. (max 709.1) 
#charge of solute molecule  = 0
#multiplicity of solute molecule  = 1
#size of solute molecule    = 32
#number of solute molecules = 1
#number of water molecules  = 56
#volume of water molecules  = 1660.6 angstrom cubed.
#volume of solute molecules = 549.8 angstrom cubed.
#volume of unit cell       = 2210.3 angstrom cubed.
#side length of water-only cubic cell = 11.842 angstrom 
#side length of cubic cell            = 13.026 angstrom 

#Unit Cell Input Option:
#inputed unitcell vectors:
#     a1  = 8.485 0.000 0.000 angstrom 
#     a2  = -4.243 7.348 0.000 angstrom 
#     a3  = 0.000 0.000 16.928 angstrom 
#inputed volume of unit cell          = 1055.5 angstrom cubed.
#volume of solute molecules = 549.8 angstrom cubed.
#volume of water molecules  = 505.7 angstrom cubed.
#effective molarity         = 3.283
#number of water molecules  = 17
#size of solvent box = 49

##################### Start of AIMD-MM NWChem Input Deck ######################
#solute =  xyzdata{Pt 1.41421 0.81650 2.30940 | Pt -4.24264 0.81650 2.30940 | Pt -1.41421 0.81650 2.30940 | Pt -2.82843 3.26599 2.30940 | Pt 0.00000 3.26599 2.30940 | Pt -1.41421 2.44949 0.00000 | Pt 1.41421 2.44949 0.00000 | Pt -5.65685 3.26599 2.30940 | Pt -4.24264 2.44949 0.00000 | Pt 0.00000 -1.63299 2.30940 | Pt 2.82843 -1.63299 2.30940 | Pt 1.41421 -2.44949 0.00000 | Pt 4.24264 -2.44949 0.00000 | Pt 2.82843 0.00000 0.00000 | Pt 4.24264 -0.81650 -2.30940 | Pt -2.82843 -1.63299 2.30940 | Pt -1.41421 -2.44949 0.00000 | Pt -2.82843 0.00000 0.00000 | Pt 0.00000 0.00000 0.00000 | Pt -1.41421 -0.81650 -2.30940 | Pt 1.41421 -0.81650 -2.30940 | Pt 0.00000 1.63299 -2.30940 | Pt 2.82843 1.63299 -2.30940 | Pt -2.82843 1.63299 -2.30940 | Pt 2.82843 -3.26599 -2.30940 | Pt 5.65685 -3.26599 -2.30940 | Pt 0.00000 -3.26599 -2.30940 | C -0.79119 0.77725 4.48215 | H -0.79119 -0.11275 3.85285 | H -0.79119 1.66725 3.85285 | H -1.68119 0.77725 5.11145 | H 0.09881 0.77725 5.11145}  theory{aimd-mm}  ^{0}  mult{1} unitcell{lattice_vectors | 8.485281 0.000000 0.000000 | -4.242641 7.348469 0.000000 | 0.000000 0.000000 16.928203}  

title "tequil 300K  solute + 17 water aimdmm simulation" 

memory 1900 mb

start solutesolvent

#permanent_dir ./perm
#scratch_dir   ./perm

charge 0
geometry noautosym noautoz
Pt  1.414210 0.816500 2.309400
Pt  -4.242640 0.816500 2.309400
Pt  -1.414210 0.816500 2.309400
Pt  -2.828430 3.265990 2.309400
Pt  0.000000 3.265990 2.309400
Pt  -1.414210 2.449490 0.000000
Pt  1.414210 2.449490 0.000000
Pt  -5.656850 3.265990 2.309400
Pt  -4.242640 2.449490 0.000000
Pt  0.000000 -1.632990 2.309400
Pt  2.828430 -1.632990 2.309400
Pt  1.414210 -2.449490 0.000000
Pt  4.242640 -2.449490 0.000000
Pt  2.828430 0.000000 0.000000
Pt  4.242640 -0.816500 -2.309400
Pt  -2.828430 -1.632990 2.309400
Pt  -1.414210 -2.449490 0.000000
Pt  -2.828430 0.000000 0.000000
Pt  0.000000 0.000000 0.000000
Pt  -1.414210 -0.816500 -2.309400
Pt  1.414210 -0.816500 -2.309400
Pt  0.000000 1.632990 -2.309400
Pt  2.828430 1.632990 -2.309400
Pt  -2.828430 1.632990 -2.309400
Pt  2.828430 -3.265990 -2.309400
Pt  5.656850 -3.265990 -2.309400
Pt  0.000000 -3.265990 -2.309400
C  -0.791190 0.777250 4.482150
H  -0.791190 -0.112750 3.852850
H  -0.791190 1.667250 3.852850
H  -1.681190 0.777250 5.111450
H  0.098810 0.777250 5.111450
O  -0.196461 3.183388 -6.157194
H  0.803539 3.183388 -6.157194
H  -0.529445 4.126320 -6.157194
O  1.586095 -3.149555 8.072190
H  2.586095 -3.149555 8.072190
H  1.253111 -2.206623 8.072190
O  5.468769 -2.354939 7.802585
H  6.468769 -2.354939 7.802585
H  5.135785 -1.412007 7.802585
O  0.243378 0.107343 -4.948632
H  1.243378 0.107343 -4.948632
H  -0.089606 1.050276 -4.948632
O  1.625572 1.171100 7.621897
H  2.625572 1.171100 7.621897
H  1.292588 2.114032 7.621897
O  -0.194645 -2.802220 -5.515839
H  0.805355 -2.802220 -5.515839
H  -0.527630 -1.859287 -5.515839
O  -4.089507 -0.234851 -8.222958
H  -3.089507 -0.234851 -8.222958
H  -4.422492 0.708081 -8.222958
O  -0.503222 -3.183474 5.364007
H  0.496778 -3.183474 5.364007
H  -0.836206 -2.240542 5.364007
O  -2.613851 2.402491 -6.983756
H  -1.613851 2.402491 -6.983756
H  -2.946835 3.345423 -6.983756
O  -0.796039 2.156594 7.602149
H  0.203961 2.156594 7.602149
H  -1.129023 3.099526 7.602149
O  0.691102 3.051564 5.409400
H  1.691102 3.051564 5.409400
H  0.358118 3.994497 5.409400
O  -2.468818 -1.557504 -5.906760
H  -1.468818 -1.557504 -5.906760
H  -2.801803 -0.614571 -5.906760
O  3.434614 -2.194360 6.018503
H  4.434614 -2.194360 6.018503
H  3.101630 -1.251428 6.018503
O  3.591956 1.077833 -5.422119
H  4.591956 1.077833 -5.422119
H  3.258971 2.020766 -5.422119
O  2.351562 -1.438611 -6.969290
H  3.351562 -1.438611 -6.969290
H  2.018578 -0.495679 -6.969290
O  3.209054 1.128019 5.461550
H  4.209054 1.128019 5.461550
H  2.876070 2.070951 5.461550
O  0.009205 0.049123 -7.640089
H  1.009205 0.049123 -7.640089
H  -0.323779 0.992055 -7.640089
end

set nwpw:cif_filename solutesolvent

nwpw
   simulation_cell
      lattice_vectors
          16.034864 0.000000 0.000000
          -8.017433 13.886599 0.000000
          0.000000 0.000000 31.989680

   end
   qmmm
      mm_tags 33:83
      lj_ion_parameters Pt 3.500000 0.100000
      lj_ion_parameters C 3.410000 0.100000
      lj_ion_parameters H 0.700000 0.044000
      lj_ion_parameters O^ 3.165558 0.155394

      fragment spc
         size 3
         index_start 33:81:3

         #spc/e water
         shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0

         #Toukan-Rahman Potential
         #bond_morse  1 2    0.1623940 1.3578682  1.889726878
         #bond_morse  1 3    0.1623940 1.3578682  1.889726878
         #bond_spring 2 3    0.0733187 3.0864590
         #cross_bond_spring 1 2 1.889726878 2 3 3.0864590 -0.0943540
         #cross_bond_spring 1 3 1.889726878 2 3 3.0864590 -0.0943540
         #cross_bond_spring 1 2 1.889726878 1 3 1.889726878 0.0498426
      end
   end
   xc pbe
   mult 1
   cutoff 2.0
   lmbfgs
end

set geometry:actlist 33:83
task pspw noit_energy

task pspw gradient

nwpw; steepest_descent; geometry_optimize; time_step 1.0e-9; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-8; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-7; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-6; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-5; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-4; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-3; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-2; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0e-1; loop 10 10; end; end; task pspw steepest_descent
nwpw; steepest_descent; geometry_optimize; time_step 1.0;    loop 10 10; end; end; task pspw steepest_descent

nwpw
   car-parrinello
      temperature 400.0
      time_step 5.0
      fake_mass 750.0
      loop 10 1000
      xyz_filename        startl-2020-1-3-10.xyz
      emotion_filename    startl-2020-1-3-10.emotion
      ion_motion_filename startl-2020-1-3-10.ion_motion
   end
end
task pspw car-parrinello


unset geometry:actlist
nwpw
   lmbfgs
   xc pbe
   cutoff 50.0
end
task pspw gradient

nwpw
   car-parrinello
      temperature 300.0 start
      time_step 5.0
      fake_mass 750.0
      loop 10 1000
      xyz_filename        tequil-2020-1-3-10.xyz
      emotion_filename    tequil-2020-1-3-10.emotion
      ion_motion_filename tequil-2020-1-3-10.ion_motion
      fei                 tequil-2020-1-3-10.fei
   end
end
task pspw car-parrinello

nwpw
   car-parrinello
      temperature 300.0 restart
   end
end
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
task pspw car-parrinello
##################### End of AIMD-MM NWChem Input Deck ######################
# queue_name: nwchem :queue_name
# label:nwchem-49.nw mytest curdir=we31869.emsl.pnl.gov:/media/seagate2/Projects/Other/C1H4Pt27-aimdmm :label

#########################  END   NWCHEM INPUT DECK - NWJOB 266022 ########################