Commit d04ea865 authored by Tonnam Balankura's avatar Tonnam Balankura
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add examples for pair_zhou

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pair_style zhou example
=================

This folder contains a example of the use of pair_style zhou for system
containing Ag, ethylene glycol (EG) and polyvinylpyrrolidone (PVP).
The pair_style is designed for the interaction between metals and organic
compounds. For this Ag-EG-PVP system, we use pair_style zhou for the
interaction between Ag and the oxygen atom in EG and PVP, as described in
the publication listed below.

Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn.
"A force field for describing the polyvinylpyrrolidone-mediated solution-phase
synthesis of shape-selective Ag nanoparticles."
The Journal of Physical Chemistry C 118, no. 6 (2014): 3366-3374.
http://pubs.acs.org/doi/abs/10.1021/jp412098n

Other potentials used for this Ag-EG-PVP system includes the
EAM, Morse, and CHARMM potential. We note that the EAM potential file,
'Ag_O1X5.5_O2X0.55.eam.fs', also contains the information about the
one-way electron density donation from the oxygen atoms to Ag atoms.
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# ----------------- Settings Section -----------------

units           metal 
boundary        p p p
neigh_modify    delay 0 every 1 check yes

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
pair_style      hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 zhou 12.0 0.75 20.0 morse 5.5
kspace_style    pppm 1e-4

# ----------------- Atom Definition Section -----------------

read_data system.data

pair_coeff   *   *  eam/fs Ag_O1X5.5_O2X0.55.eam.fs NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL O1 NULL NULL NULL O2 Ag
pair_coeff  1*4   16     morse   0.00480  1.30   1.94 # HGA1, HGA2, HGA3
pair_coeff    5   16     morse   0.00722  1.14   4.85 # CG2R53  
pair_coeff  6*8   16     morse   0.00244  1.01   4.92 # CG311, CG321, CG331
pair_coeff    9   16     morse   0.00230  1.03   4.92 # CG3C52
pair_coeff   10   16     morse   0.00492  1.76   3.26 # NG2R53
pair_coeff   11   16     morse   0.00325  3.34   2.65 # OG2D1
pair_coeff   12   16     morse   0.00480  1.30   1.94 # HCA2
pair_coeff   13   16     morse   0.00448  1.06   2.13 # HCP1
pair_coeff   14   16     morse   0.00216  1.26   4.99 # CC32A
pair_coeff   15   16     morse   0.00217  2.09   3.43 # OC311
pair_coeff  1*4   16     zhou    0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff  5*9   16     zhou    0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff   10   16     zhou    0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff   11   16     zhou    0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff   12   16     zhou    0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff   13   16     zhou    0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff   14   16     zhou    0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff   15   16     zhou    0.0 1.0 1.0 22.9973 2.702 # OC311

# arithmetic mixing for CHARMM pair coeffs
pair_coeff   1   1  lj/charmm/coul/long    0.001520  2.387609  0.001520  2.387609 #HRA2  HRA2  
pair_coeff   1   2  lj/charmm/coul/long    0.001722  2.387609  0.001722  2.387609 #HRA2  HGA1  
pair_coeff   1   3  lj/charmm/coul/long    0.001520  2.387609  0.001520  2.387609 #HRA2  HGA2  
pair_coeff   1   4  lj/charmm/coul/long    0.001257  2.387609  0.001257  2.387609 #HRA2  HGA3  
pair_coeff   1   5  lj/charmm/coul/long    0.001150  3.153782  0.001150  3.153782 #HRA2  CG2R53
pair_coeff   1   6  lj/charmm/coul/long    0.001454  2.975602  0.000808  2.886512 #HRA2  CG311 
pair_coeff   1   7  lj/charmm/coul/long    0.001922  2.984511  0.000808  2.886512 #HRA2  CG321 
pair_coeff   1   8  lj/charmm/coul/long    0.002267  3.020147  0.000808  2.886512 #HRA2  CG331 
pair_coeff   1   9  lj/charmm/coul/long    0.001988  2.993420  0.000808  2.886512 #HRA2  CG3C52
pair_coeff   1  10  lj/charmm/coul/long    0.003630  2.841967  0.003630  2.841967 #HRA2  NG2R53
pair_coeff   1  11  lj/charmm/coul/long    0.002811  2.708333  0.002811  2.441063 #HRA2  OG2D1 
pair_coeff   1  12  lj/charmm/coul/long    0.001520  2.387609  0.001520  2.387609 #HRA2  HCA2  
pair_coeff   1  13  lj/charmm/coul/long    0.001739  1.393811  0.001739  1.393811 #HRA2  HCP1  
pair_coeff   1  14  lj/charmm/coul/long    0.001922  2.984511  0.000808  2.886512 #HRA2  CC32A 
pair_coeff   1  15  lj/charmm/coul/long    0.003558  2.766240  0.003558  2.766240 #HRA2  OC311 
pair_coeff   2   2  lj/charmm/coul/long    0.001950  2.387609  0.001950  2.387609 #HGA1  HGA1  
pair_coeff   2   3  lj/charmm/coul/long    0.001722  2.387609  0.001722  2.387609 #HGA1  HGA2  
pair_coeff   2   4  lj/charmm/coul/long    0.001424  2.387609  0.001424  2.387609 #HGA1  HGA3  
pair_coeff   2   5  lj/charmm/coul/long    0.001302  3.153782  0.001302  3.153782 #HGA1  CG2R53
pair_coeff   2   6  lj/charmm/coul/long    0.001646  2.975602  0.000916  2.886512 #HGA1  CG311 
pair_coeff   2   7  lj/charmm/coul/long    0.002177  2.984511  0.000916  2.886512 #HGA1  CG321 
pair_coeff   2   8  lj/charmm/coul/long    0.002567  3.020147  0.000916  2.886512 #HGA1  CG331 
pair_coeff   2   9  lj/charmm/coul/long    0.002252  2.993420  0.000916  2.886512 #HGA1  CG3C52
pair_coeff   2  10  lj/charmm/coul/long    0.004112  2.841967  0.004112  2.841967 #HGA1  NG2R53
pair_coeff   2  11  lj/charmm/coul/long    0.003184  2.708333  0.003184  2.441063 #HGA1  OG2D1 
pair_coeff   2  12  lj/charmm/coul/long    0.001722  2.387609  0.001722  2.387609 #HGA1  HCA2  
pair_coeff   2  13  lj/charmm/coul/long    0.001970  1.393811  0.001970  1.393811 #HGA1  HCP1  
pair_coeff   2  14  lj/charmm/coul/long    0.002177  2.984511  0.000916  2.886512 #HGA1  CC32A 
pair_coeff   2  15  lj/charmm/coul/long    0.004030  2.766240  0.004030  2.766240 #HGA1  OC311 
pair_coeff   3   3  lj/charmm/coul/long    0.001520  2.387609  0.001520  2.387609 #HGA2  HGA2  
pair_coeff   3   4  lj/charmm/coul/long    0.001257  2.387609  0.001257  2.387609 #HGA2  HGA3  
pair_coeff   3   5  lj/charmm/coul/long    0.001150  3.153782  0.001150  3.153782 #HGA2  CG2R53
pair_coeff   3   6  lj/charmm/coul/long    0.001454  2.975602  0.000808  2.886512 #HGA2  CG311 
pair_coeff   3   7  lj/charmm/coul/long    0.001922  2.984511  0.000808  2.886512 #HGA2  CG321 
pair_coeff   3   8  lj/charmm/coul/long    0.002267  3.020147  0.000808  2.886512 #HGA2  CG331 
pair_coeff   3   9  lj/charmm/coul/long    0.001988  2.993420  0.000808  2.886512 #HGA2  CG3C52
pair_coeff   3  10  lj/charmm/coul/long    0.003630  2.841967  0.003630  2.841967 #HGA2  NG2R53
pair_coeff   3  11  lj/charmm/coul/long    0.002811  2.708333  0.002811  2.441063 #HGA2  OG2D1 
pair_coeff   3  12  lj/charmm/coul/long    0.001520  2.387609  0.001520  2.387609 #HGA2  HCA2  
pair_coeff   3  13  lj/charmm/coul/long    0.001739  1.393811  0.001739  1.393811 #HGA2  HCP1  
pair_coeff   3  14  lj/charmm/coul/long    0.001922  2.984511  0.000808  2.886512 #HGA2  CC32A 
pair_coeff   3  15  lj/charmm/coul/long    0.003558  2.766240  0.003558  2.766240 #HGA2  OC311 
pair_coeff   4   4  lj/charmm/coul/long    0.001040  2.387609  0.001040  2.387609 #HGA3  HGA3  
pair_coeff   4   5  lj/charmm/coul/long    0.000951  3.153782  0.000951  3.153782 #HGA3  CG2R53
pair_coeff   4   6  lj/charmm/coul/long    0.001202  2.975602  0.000669  2.886512 #HGA3  CG311 
pair_coeff   4   7  lj/charmm/coul/long    0.001590  2.984511  0.000669  2.886512 #HGA3  CG321 
pair_coeff   4   8  lj/charmm/coul/long    0.001875  3.020147  0.000669  2.886512 #HGA3  CG331 
pair_coeff   4   9  lj/charmm/coul/long    0.001644  2.993420  0.000669  2.886512 #HGA3  CG3C52
pair_coeff   4  10  lj/charmm/coul/long    0.003003  2.841967  0.003003  2.841967 #HGA3  NG2R53
pair_coeff   4  11  lj/charmm/coul/long    0.002326  2.708333  0.002326  2.441063 #HGA3  OG2D1 
pair_coeff   4  12  lj/charmm/coul/long    0.001257  2.387609  0.001257  2.387609 #HGA3  HCA2  
pair_coeff   4  13  lj/charmm/coul/long    0.001439  1.393811  0.001439  1.393811 #HGA3  HCP1  
pair_coeff   4  14  lj/charmm/coul/long    0.001590  2.984511  0.000669  2.886512 #HGA3  CC32A 
pair_coeff   4  15  lj/charmm/coul/long    0.002943  2.766240  0.002943  2.766240 #HGA3  OC311 
pair_coeff   5   5  lj/charmm/coul/long    0.000870  3.919954  0.000870  3.919954 #CG2R53CG2R53
pair_coeff   5   6  lj/charmm/coul/long    0.001100  3.741775  0.000612  3.652685 #CG2R53CG311 
pair_coeff   5   7  lj/charmm/coul/long    0.001454  3.750684  0.000612  3.652685 #CG2R53CG321 
pair_coeff   5   8  lj/charmm/coul/long    0.001715  3.786320  0.000612  3.652685 #CG2R53CG331 
pair_coeff   5   9  lj/charmm/coul/long    0.001504  3.759593  0.000612  3.652685 #CG2R53CG3C52
pair_coeff   5  10  lj/charmm/coul/long    0.002746  3.608140  0.002746  3.608140 #CG2R53NG2R53
pair_coeff   5  11  lj/charmm/coul/long    0.002127  3.474505  0.002127  3.207235 #CG2R53OG2D1 
pair_coeff   5  12  lj/charmm/coul/long    0.001150  3.153782  0.001150  3.153782 #CG2R53HCA2  
pair_coeff   5  13  lj/charmm/coul/long    0.001316  2.159984  0.001316  2.159984 #CG2R53HCP1  
pair_coeff   5  14  lj/charmm/coul/long    0.001454  3.750684  0.000612  3.652685 #CG2R53CC32A 
pair_coeff   5  15  lj/charmm/coul/long    0.002692  3.532413  0.002692  3.532413 #CG2R53OC311 
pair_coeff   6   6  lj/charmm/coul/long    0.001390  3.563595  0.000430  3.385415 #CG311 CG311 
pair_coeff   6   7  lj/charmm/coul/long    0.001838  3.572504  0.000430  3.385415 #CG311 CG321 
pair_coeff   6   8  lj/charmm/coul/long    0.002168  3.608140  0.000430  3.385415 #CG311 CG331 
pair_coeff   6   9  lj/charmm/coul/long    0.001901  3.581413  0.000430  3.385415 #CG311 CG3C52
pair_coeff   6  10  lj/charmm/coul/long    0.003471  3.429960  0.001931  3.340870 #CG311 NG2R53
pair_coeff   6  11  lj/charmm/coul/long    0.002688  3.296326  0.001495  2.939966 #CG311 OG2D1 
pair_coeff   6  12  lj/charmm/coul/long    0.001454  2.975602  0.000808  2.886512 #CG311 HCA2  
pair_coeff   6  13  lj/charmm/coul/long    0.001663  1.981804  0.000925  1.892714 #CG311 HCP1  
pair_coeff   6  14  lj/charmm/coul/long    0.001838  3.572504  0.000430  3.385415 #CG311 CC32A 
pair_coeff   6  15  lj/charmm/coul/long    0.003403  3.354233  0.001893  3.265143 #CG311 OC311 
pair_coeff   7   7  lj/charmm/coul/long    0.002430  3.581413  0.000430  3.385415 #CG321 CG321 
pair_coeff   7   8  lj/charmm/coul/long    0.002866  3.617049  0.000430  3.385415 #CG321 CG331 
pair_coeff   7   9  lj/charmm/coul/long    0.002514  3.590322  0.000430  3.385415 #CG321 CG3C52
pair_coeff   7  10  lj/charmm/coul/long    0.004590  3.438869  0.001931  3.340870 #CG321 NG2R53
pair_coeff   7  11  lj/charmm/coul/long    0.003555  3.305235  0.001495  2.939966 #CG321 OG2D1 
pair_coeff   7  12  lj/charmm/coul/long    0.001922  2.984511  0.000808  2.886512 #CG321 HCA2  
pair_coeff   7  13  lj/charmm/coul/long    0.002199  1.990713  0.000925  1.892714 #CG321 HCP1  
pair_coeff   7  14  lj/charmm/coul/long    0.002430  3.581413  0.000430  3.385415 #CG321 CC32A 
pair_coeff   7  15  lj/charmm/coul/long    0.004499  3.363142  0.001893  3.265143 #CG321 OC311 
pair_coeff   8   8  lj/charmm/coul/long    0.003380  3.652685  0.000430  3.385415 #CG331 CG331 
pair_coeff   8   9  lj/charmm/coul/long    0.002964  3.625958  0.000430  3.385415 #CG331 CG3C52
pair_coeff   8  10  lj/charmm/coul/long    0.005413  3.474505  0.001931  3.340870 #CG331 NG2R53
pair_coeff   8  11  lj/charmm/coul/long    0.004192  3.340871  0.001495  2.939966 #CG331 OG2D1 
pair_coeff   8  12  lj/charmm/coul/long    0.002267  3.020147  0.000808  2.886512 #CG331 HCA2  
pair_coeff   8  13  lj/charmm/coul/long    0.002593  2.026349  0.000925  1.892714 #CG331 HCP1  
pair_coeff   8  14  lj/charmm/coul/long    0.002866  3.617049  0.000430  3.385415 #CG331 CC32A 
pair_coeff   8  15  lj/charmm/coul/long    0.005306  3.398778  0.001893  3.265143 #CG331 OC311 
pair_coeff   9   9  lj/charmm/coul/long    0.002600  3.599231  0.000430  3.385415 #CG3C52CG3C52
pair_coeff   9  10  lj/charmm/coul/long    0.004748  3.447778  0.001931  3.340870 #CG3C52NG2R53
pair_coeff   9  11  lj/charmm/coul/long    0.003677  3.314144  0.001495  2.939966 #CG3C52OG2D1 
pair_coeff   9  12  lj/charmm/coul/long    0.001988  2.993420  0.000808  2.886512 #CG3C52HCA2  
pair_coeff   9  13  lj/charmm/coul/long    0.002275  1.999622  0.000925  1.892714 #CG3C52HCP1  
pair_coeff   9  14  lj/charmm/coul/long    0.002514  3.590322  0.000430  3.385415 #CG3C52CC32A 
pair_coeff   9  15  lj/charmm/coul/long    0.004654  3.372051  0.001893  3.265143 #CG3C52OC311 
pair_coeff  10  10  lj/charmm/coul/long    0.008670  3.296325  0.008670  3.296325 #NG2R53NG2R53
pair_coeff  10  11  lj/charmm/coul/long    0.006714  3.162691  0.006714  2.895421 #NG2R53OG2D1 
pair_coeff  10  12  lj/charmm/coul/long    0.003630  2.841967  0.003630  2.841967 #NG2R53HCA2  
pair_coeff  10  13  lj/charmm/coul/long    0.004154  1.848169  0.004154  1.848169 #NG2R53HCP1  
pair_coeff  10  14  lj/charmm/coul/long    0.004590  3.438869  0.001931  3.340870 #NG2R53CC32A 
pair_coeff  10  15  lj/charmm/coul/long    0.008498  3.220598  0.008498  3.220598 #NG2R53OC311 
pair_coeff  11  11  lj/charmm/coul/long    0.005200  3.029056  0.005200  2.494516 #OG2D1 OG2D1 
pair_coeff  11  12  lj/charmm/coul/long    0.002811  2.708333  0.002811  2.441063 #OG2D1 HCA2  
pair_coeff  11  13  lj/charmm/coul/long    0.003217  1.714535  0.003217  1.447265 #OG2D1 HCP1  
pair_coeff  11  14  lj/charmm/coul/long    0.003555  3.305235  0.001495  2.939966 #OG2D1 CC32A 
pair_coeff  11  15  lj/charmm/coul/long    0.006581  3.086964  0.006581  2.819694 #OG2D1 OC311 
pair_coeff  12  12  lj/charmm/coul/long    0.001520  2.387609  0.001520  2.387609 #HCA2  HCA2  
pair_coeff  12  13  lj/charmm/coul/long    0.001739  1.393811  0.001739  1.393811 #HCA2  HCP1  
pair_coeff  12  14  lj/charmm/coul/long    0.001922  2.984511  0.000808  2.886512 #HCA2  CC32A 
pair_coeff  12  15  lj/charmm/coul/long    0.003558  2.766240  0.003558  2.766240 #HCA2  OC311 
pair_coeff  13  13  lj/charmm/coul/long    0.001990  0.400014  0.001990  0.400014 #HCP1  HCP1  
pair_coeff  13  14  lj/charmm/coul/long    0.002199  1.990713  0.000925  1.892714 #HCP1  CC32A 
pair_coeff  13  15  lj/charmm/coul/long    0.004071  1.772443  0.004071  1.772443 #HCP1  OC311 
pair_coeff  14  14  lj/charmm/coul/long    0.002430  3.581413  0.000430  3.385415 #CC32A CC32A 
pair_coeff  14  15  lj/charmm/coul/long    0.004499  3.363142  0.001893  3.265143 #CC32A OC311 
pair_coeff  15  15  lj/charmm/coul/long    0.008330  3.144872  0.008330  3.144872 #OC311 OC311 


special_bonds   charmm

# ----------------- Run Section -----------------

timestep        0.001

restart         2000 NVT.restart.1_dup NVT.restart.1

minimize		1.0e-5 1.0e-7 1000 10000

velocity        all create 413.0 12378 dist gaussian

thermo          0
thermo_style    custom step pe ke etotal temp vol press lx lz pxx pyy pzz
thermo_modify   flush yes

variable STEP equal step
variable PE equal pe
variable KE equal ke
variable ETOTAL equal etotal
variable TEMP equal temp
variable VOL equal vol
variable PRESS equal press
variable LX equal lx
variable LZ equal lz
variable PXX equal pxx
variable PYY equal pyy
variable PZZ equal pzz

fix             1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
fix 			thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"

dump		    1 all custom 200000 traj_npt.lammpstrj id mol type x y z ix iy iz

run             15000000