add examples for pair_zhou (d04ea865) · Commits · 郑智淋 / lammps

examples/USER/misc/zhou/Ag_O1X5.5_O2X0.55.eam.fs

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examples/USER/misc/zhou/README

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Original line number	Diff line number	Diff line
		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.

examples/USER/misc/zhou/system.data

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examples/USER/misc/zhou/system.in

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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

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