forked from lijiext/lammps
Merge branch 'add-pair-zhou' of https://github.com/tonnamb/lammps into pull-417
This commit is contained in:
Axel Kohlmeyer
commit
43f27250b5
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\documentclass[12pt,fleqn]{article}
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\usepackage{amsmath}
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\thispagestyle{empty}
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\begin{document}
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\setlength{\jot}{2ex}
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\begin{gather*}
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E = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\
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f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}}
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\end{gather*}
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\end{document}
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@ -1061,7 +1061,8 @@ package"_Section_start.html#start_3.
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"table/rx"_pair_table_rx.html,
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"tersoff/table (o)"_pair_tersoff.html,
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"thole"_pair_thole.html,
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"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
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"tip4p/long/soft (o)"_pair_lj_soft.html,
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"zhou"_pair_zhou.html :tb(c=4,ea=c)
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:line
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@ -0,0 +1,56 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style zhou command :h3
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[Syntax:]
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pair_style zhou cutoff s6 d :pre
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cutoff = global cutoff (distance units)
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s6 = global scaling factor of the exchange-correlation functional used (unitless)
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d = damping scaling factor of Grimme's method (unitless) :ul
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[Examples:]
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pair_style zhou 12.0 0.75 20.0
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pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 zhou 12.0 0.75 20.0 morse 5.5 :pre
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pair_coeff 1 2 zhou 0.0 1.0 1.0 10.2847 2.361 :pre
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[Description:]
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Style {zhou} computes pairwise van der Waals (vdW) interactions using the
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"(Grimme)"_#Grimme method implemented in the Many-Body Metal-Organic (MOMB)
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force field described extensively in "(Fichthorn)"_#Fichthorn and
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"(Zhou)"_#Zhou. This potential is widely used to correct for dispersion
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in density functional theory calculations.
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:c,image(Eqs/pair_zhou.jpg)
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For the {zhou} pair style, the following coefficients must be defined for each
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pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the
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examples above, or in the data file or restart files read by the
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"read_data"_read_data.html as described below:
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D0 (energy units)
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alpha (1/distance units)
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r0 (distance units)
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C6 (energy*distance^6 units)
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Rr (distance units) :ul
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:line
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:link(Grimme)
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[(Grimme)] Grimme, J Comput Chem, 27(15), 1787-1799 (2006).
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:link(Fichthorn)
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[(Fichthorn)] Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016).
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:link(Zhou)
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[(Zhou)] Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014).
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@ -101,5 +101,6 @@ Pair Styles :h1
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pair_yukawa_colloid
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pair_zbl
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pair_zero
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pair_zhou
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END_RST -->
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,20 @@
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pair_style zhou example
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=================
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This folder contains a example of the use of pair_style zhou for system
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containing Ag, ethylene glycol (EG) and polyvinylpyrrolidone (PVP).
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The pair_style is designed for the interaction between metals and organic
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compounds. For this Ag-EG-PVP system, we use pair_style zhou for the
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interaction between Ag and the oxygen atom in EG and PVP, as described in
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the publication listed below.
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Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn.
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"A force field for describing the polyvinylpyrrolidone-mediated solution-phase
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synthesis of shape-selective Ag nanoparticles."
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The Journal of Physical Chemistry C 118, no. 6 (2014): 3366-3374.
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http://pubs.acs.org/doi/abs/10.1021/jp412098n
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Other potentials used for this Ag-EG-PVP system includes the
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EAM, Morse, and CHARMM potential. We note that the EAM potential file,
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'Ag_O1X5.5_O2X0.55.eam.fs', also contains the information about the
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one-way electron density donation from the oxygen atoms to Ag atoms.
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,197 @@
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# ----------------- Settings Section -----------------
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units metal
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boundary p p p
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neigh_modify delay 0 every 1 check yes
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 zhou 12.0 0.75 20.0 morse 5.5
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kspace_style pppm 1e-4
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# ----------------- Atom Definition Section -----------------
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read_data system.data
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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
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pair_coeff 1*4 16 morse 0.00480 1.30 1.94 # HGA1, HGA2, HGA3
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pair_coeff 5 16 morse 0.00722 1.14 4.85 # CG2R53
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pair_coeff 6*8 16 morse 0.00244 1.01 4.92 # CG311, CG321, CG331
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pair_coeff 9 16 morse 0.00230 1.03 4.92 # CG3C52
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pair_coeff 10 16 morse 0.00492 1.76 3.26 # NG2R53
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pair_coeff 11 16 morse 0.00325 3.34 2.65 # OG2D1
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pair_coeff 12 16 morse 0.00480 1.30 1.94 # HCA2
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pair_coeff 13 16 morse 0.00448 1.06 2.13 # HCP1
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pair_coeff 14 16 morse 0.00216 1.26 4.99 # CC32A
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pair_coeff 15 16 morse 0.00217 2.09 3.43 # OC311
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pair_coeff 1*4 16 zhou 0.0 1.0 1.0 10.2847 2.361 # H
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pair_coeff 5*9 16 zhou 0.0 1.0 1.0 36.3619 2.812 # C
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pair_coeff 10 16 zhou 0.0 1.0 1.0 30.4846 2.757 # N
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pair_coeff 11 16 zhou 0.0 1.0 1.0 22.9973 2.702 # O
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pair_coeff 12 16 zhou 0.0 1.0 1.0 10.2847 2.361 # HCA2
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pair_coeff 13 16 zhou 0.0 1.0 1.0 10.2847 2.361 # HCP1
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pair_coeff 14 16 zhou 0.0 1.0 1.0 36.3619 2.812 # CC32A
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pair_coeff 15 16 zhou 0.0 1.0 1.0 22.9973 2.702 # OC311
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# arithmetic mixing for CHARMM pair coeffs
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pair_coeff 1 1 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HRA2
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pair_coeff 1 2 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HRA2 HGA1
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||||
pair_coeff 1 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HGA2
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||||
pair_coeff 1 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HRA2 HGA3
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||||
pair_coeff 1 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HRA2 CG2R53
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pair_coeff 1 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HRA2 CG311
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pair_coeff 1 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CG321
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pair_coeff 1 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HRA2 CG331
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||||
pair_coeff 1 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HRA2 CG3C52
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||||
pair_coeff 1 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HRA2 NG2R53
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||||
pair_coeff 1 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HRA2 OG2D1
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pair_coeff 1 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HCA2
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||||
pair_coeff 1 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HRA2 HCP1
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||||
pair_coeff 1 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CC32A
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pair_coeff 1 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HRA2 OC311
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pair_coeff 2 2 lj/charmm/coul/long 0.001950 2.387609 0.001950 2.387609 #HGA1 HGA1
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pair_coeff 2 3 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HGA2
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pair_coeff 2 4 lj/charmm/coul/long 0.001424 2.387609 0.001424 2.387609 #HGA1 HGA3
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pair_coeff 2 5 lj/charmm/coul/long 0.001302 3.153782 0.001302 3.153782 #HGA1 CG2R53
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pair_coeff 2 6 lj/charmm/coul/long 0.001646 2.975602 0.000916 2.886512 #HGA1 CG311
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||||
pair_coeff 2 7 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CG321
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pair_coeff 2 8 lj/charmm/coul/long 0.002567 3.020147 0.000916 2.886512 #HGA1 CG331
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||||
pair_coeff 2 9 lj/charmm/coul/long 0.002252 2.993420 0.000916 2.886512 #HGA1 CG3C52
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||||
pair_coeff 2 10 lj/charmm/coul/long 0.004112 2.841967 0.004112 2.841967 #HGA1 NG2R53
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||||
pair_coeff 2 11 lj/charmm/coul/long 0.003184 2.708333 0.003184 2.441063 #HGA1 OG2D1
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||||
pair_coeff 2 12 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HCA2
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||||
pair_coeff 2 13 lj/charmm/coul/long 0.001970 1.393811 0.001970 1.393811 #HGA1 HCP1
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||||
pair_coeff 2 14 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CC32A
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||||
pair_coeff 2 15 lj/charmm/coul/long 0.004030 2.766240 0.004030 2.766240 #HGA1 OC311
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||||
pair_coeff 3 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HGA2
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||||
pair_coeff 3 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA2 HGA3
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||||
pair_coeff 3 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HGA2 CG2R53
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||||
pair_coeff 3 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HGA2 CG311
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||||
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
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pair_coeff 3 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HGA2 CG3C52
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pair_coeff 3 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HGA2 NG2R53
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||||
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
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||||
pair_coeff 3 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CC32A
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||||
pair_coeff 3 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HGA2 OC311
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||||
pair_coeff 4 4 lj/charmm/coul/long 0.001040 2.387609 0.001040 2.387609 #HGA3 HGA3
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||||
pair_coeff 4 5 lj/charmm/coul/long 0.000951 3.153782 0.000951 3.153782 #HGA3 CG2R53
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pair_coeff 4 6 lj/charmm/coul/long 0.001202 2.975602 0.000669 2.886512 #HGA3 CG311
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pair_coeff 4 7 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CG321
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||||
pair_coeff 4 8 lj/charmm/coul/long 0.001875 3.020147 0.000669 2.886512 #HGA3 CG331
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||||
pair_coeff 4 9 lj/charmm/coul/long 0.001644 2.993420 0.000669 2.886512 #HGA3 CG3C52
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||||
pair_coeff 4 10 lj/charmm/coul/long 0.003003 2.841967 0.003003 2.841967 #HGA3 NG2R53
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||||
pair_coeff 4 11 lj/charmm/coul/long 0.002326 2.708333 0.002326 2.441063 #HGA3 OG2D1
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||||
pair_coeff 4 12 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA3 HCA2
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||||
pair_coeff 4 13 lj/charmm/coul/long 0.001439 1.393811 0.001439 1.393811 #HGA3 HCP1
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||||
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
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||||
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
|
||||
|
|
@ -70,4 +70,5 @@ pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
|
|||
pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
|
||||
pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
|
||||
pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11
|
||||
pair_style zhou, Kristen Fichthorn, fichthorn@psu.edu, 18 Mar 17
|
||||
temper/grem, David Stelter, dstelter@bu.edu, 22 Nov 16
|
||||
|
|
|
|||
|
|
@ -0,0 +1,363 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
Contributed by Kristen Fichthorn @ Penn State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include "pair_zhou.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairZhou::PairZhou(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairZhou::~PairZhou()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(d0);
|
||||
memory->destroy(alpha);
|
||||
memory->destroy(r0);
|
||||
memory->destroy(c);
|
||||
memory->destroy(rr);
|
||||
memory->destroy(morse1);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r,dr,dexp,factor_lj,r2inv,r6inv,ddexp,invexp;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[itype][jtype];
|
||||
dexp = exp(-alpha[itype][jtype] * dr);
|
||||
ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0));
|
||||
invexp = 1.0/(1+ddexp);
|
||||
fpair = morse1[itype][jtype] * (dexp*dexp - dexp) / r;
|
||||
fpair -= sscale*c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r;
|
||||
fpair -= sscale*c[itype][jtype] * (6.0 * invexp * r6inv * r2inv);
|
||||
fpair *= factor_lj;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
|
||||
sscale*c[itype][jtype]*r6inv*invexp - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(d0,n+1,n+1,"pair:d0");
|
||||
memory->create(alpha,n+1,n+1,"pair:alpha");
|
||||
memory->create(r0,n+1,n+1,"pair:r0");
|
||||
memory->create(c,n+1,n+1,"pair:c");
|
||||
memory->create(rr,n+1,n+1,"pair:rr");
|
||||
memory->create(morse1,n+1,n+1,"pair:morse1");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_global = force->numeric(FLERR,arg[0]);
|
||||
sscale = force->numeric(FLERR,arg[1]);
|
||||
dscale = force->numeric(FLERR,arg[2]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i+1; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double d0_one = force->numeric(FLERR,arg[2]);
|
||||
double alpha_one = force->numeric(FLERR,arg[3]);
|
||||
double r0_one = force->numeric(FLERR,arg[4]);
|
||||
double c_one = force->numeric(FLERR,arg[5]);
|
||||
double rr_one = force->numeric(FLERR,arg[6]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 8) cut_one = force->numeric(FLERR,arg[7]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
d0[i][j] = d0_one;
|
||||
alpha[i][j] = alpha_one;
|
||||
r0[i][j] = r0_one;
|
||||
cut[i][j] = cut_one;
|
||||
c[i][j] = c_one;
|
||||
rr[i][j] = rr_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairZhou::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
|
||||
|
||||
if (offset_flag) {
|
||||
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
|
||||
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
d0[j][i] = d0[i][j];
|
||||
alpha[j][i] = alpha[i][j];
|
||||
r0[j][i] = r0[i][j];
|
||||
c[j][i] = c[i][j];
|
||||
rr[j][i] = rr[i][j];
|
||||
morse1[j][i] = morse1[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&d0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&alpha[i][j],sizeof(double),1,fp);
|
||||
fwrite(&r0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&c[i][j],sizeof(double),1,fp);
|
||||
fwrite(&rr[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&d0[i][j],sizeof(double),1,fp);
|
||||
fread(&alpha[i][j],sizeof(double),1,fp);
|
||||
fread(&r0[i][j],sizeof(double),1,fp);
|
||||
fread(&c[i][j],sizeof(double),1,fp);
|
||||
fread(&rr[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&rr[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
fwrite(&sscale,sizeof(double),1,fp);
|
||||
fwrite(&dscale,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZhou::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
fread(&sscale,sizeof(double),1,fp);
|
||||
fread(&dscale,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sscale,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&dscale,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairZhou::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[itype][jtype];
|
||||
dexp = exp(-alpha[itype][jtype] * dr);
|
||||
ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0));
|
||||
invexp = 1.0/(1+ddexp);
|
||||
fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
|
||||
fforce -= factor_lj * sscale* c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r;
|
||||
fforce -= factor_lj * sscale* c[itype][jtype] * (6.0 * invexp * r6inv * r2inv);
|
||||
|
||||
phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - sscale*c[itype][jtype]*r6inv*invexp - offset[itype][jtype];
|
||||
return factor_lj*phi;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,77 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
Contributed by Kristen Fichthorn @ Penn State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(zhou,PairZhou)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_ZHOU_H
|
||||
#define LMP_PAIR_ZHOU_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairZhou : public Pair {
|
||||
public:
|
||||
PairZhou(class LAMMPS *);
|
||||
virtual ~PairZhou();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double sscale,dscale;
|
||||
double **d0,**alpha,**r0,**c,**rr;
|
||||
double **morse1;
|
||||
double **offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue