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Merge pull request #417 from tonnamb/add-pair-zhou 

add new pair potential for metal-organic interactions - pair style momb
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sjplimp 2017-03-24 09:41:30 -06:00 committed by GitHub
parent 44841f6891 568b67eee9
commit 277b93cb89
16 changed files with 261971 additions and 1 deletions
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\documentclass[12pt,fleqn]{article}
\usepackage{amsmath}
\thispagestyle{empty}
\begin{document}
\setlength{\jot}{2ex}
\begin{gather*}
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) \\
f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}}
\end{gather*}
\end{document}

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doc/src/Section_commands.txt
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@ -1035,6 +1035,7 @@ package"_Section_start.html#start_3.
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,
"momb"_pair_momb.html,
"morse/smooth/linear"_pair_morse.html,
"morse/soft"_pair_morse.html,
"multi/lucy"_pair_multi_lucy.html,
@ -1061,7 +1062,7 @@ package"_Section_start.html#start_3.
"table/rx"_pair_table_rx.html,
"tersoff/table (o)"_pair_tersoff.html,
"thole"_pair_thole.html,
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
:line

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doc/src/lammps.book
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@ -456,6 +456,7 @@ pair_meam_spline.html
pair_meam_sw_spline.html
pair_mgpt.html
pair_mie.html
pair_momb.html
pair_morse.html
pair_multi_lucy.html
pair_multi_lucy_rx.html

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style momb command :h3
[Syntax:]
pair_style momb cutoff s6 d :pre
cutoff = global cutoff (distance units)
s6 = global scaling factor of the exchange-correlation functional used (unitless)
d = damping scaling factor of Grimme's method (unitless) :ul
[Examples:]
pair_style momb 12.0 0.75 20.0
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5 :pre
pair_coeff 1 2 momb 0.0 1.0 1.0 10.2847 2.361 :pre
[Description:]
Style {momb} computes pairwise van der Waals (vdW) and short-range interactions using the
Morse potential and "(Grimme)"_#Grimme method implemented in the Many-Body
Metal-Organic (MOMB) force field described comprehensively in "(Fichthorn)"_#Fichthorn and
"(Zhou)"_#Zhou4. Grimme's method is widely used to correct for dispersion
in density functional theory calculations.
:c,image(Eqs/pair_momb.jpg)
For the {momb} pair style, the following coefficients must be defined for each
pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the
examples above, or in the data file or restart files read by the
"read_data"_read_data.html as described below:
D0 (energy units)
alpha (1/distance units)
r0 (distance units)
C6 (energy*distance^6 units)
Rr (distance units, typically sum of atomic vdW radii) :ul
:line
[Restrictions:]
This style is part of the USER-MISC package. It is only enabled if
LAMMPS is built with that package. See the "Making of
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style morse"_pair_morse.html
[Default:] none
:line
:link(Grimme)
[(Grimme)] Grimme, J Comput Chem, 27(15), 1787-1799 (2006).
:link(Fichthorn)
[(Fichthorn)] Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016).
:link(Zhou4)
[(Zhou)] Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014).

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doc/src/pairs.txt
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@ -60,6 +60,7 @@ Pair Styles :h1
pair_meam_sw_spline
pair_mgpt
pair_mie
pair_momb
pair_morse
pair_multi_lucy
pair_multi_lucy_rx

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pair_style momb example
=================
This folder contains a example of the use of pair_style momb 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 momb 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 momb 12.0 0.75 20.0 morse 5.5
kspace_style pppm 1e-5
# ----------------- 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 momb 0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff 15 16 momb 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
minimize 1.0e-3 1.0e-5 1000 10000
reset_timestep 0
velocity all create 413.0 12378 dist gaussian
thermo 10
thermo_style custom step pe ke etotal temp press pxx pyy pzz
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 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100

360
examples/USER/misc/momb/log.17Mar2017.system.g++.1 Normal file
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@ -0,0 +1,360 @@
LAMMPS (17 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# ----------------- 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 momb 12.0 0.75 20.0 morse 5.5
kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
read_data system.data
orthogonal box = (0 0 0) to (53.6198 53.6198 160)
1 by 1 by 1 MPI processor grid
reading atoms ...
18146 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
13 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
12694 bonds
reading angles ...
19786 angles
reading dihedrals ...
29690 dihedrals
reading impropers ...
5 impropers
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
23 = max # of special neighbors
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 momb 0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff 15 16 momb 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
minimize 1.0e-3 1.0e-5 1000 10000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 79764 46656
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 8 23
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/charmm/coul/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair momb, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) pair morse, perpetual, copy from (3)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 99.82 | 99.82 | 99.82 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10035.476 218.18376 -9817.2917 -1066.914
9 0 -10244.892 211.35072 -10033.541 -3283.8636
Loop time of 2.6765 on 1 procs for 9 steps with 18146 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9817.29174185 -10023.887559 -10033.5413886
Force two-norm initial, final = 76.9233 27.3547
Force max component initial, final = 11.8658 7.37882
Final line search alpha, max atom move = 0.0472944 0.348977
Iterations, force evaluations = 9 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3191 | 2.3191 | 2.3191 | 0.0 | 86.65
Bond | 0.084626 | 0.084626 | 0.084626 | 0.0 | 3.16
Kspace | 0.2622 | 0.2622 | 0.2622 | 0.0 | 9.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0033448 | 0.0033448 | 0.0033448 | 0.0 | 0.12
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.007261 | | | 0.27
Nlocal: 18146 ave 18146 max 18146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 29277 ave 29277 max 29277 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 439189 ave 439189 max 439189 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 439189
Ave neighs/atom = 24.2031
Ave special neighs/atom = 5.92362
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
velocity all create 413.0 12378 dist gaussian
thermo 10
thermo_style custom step pe ke etotal temp press pxx pyy pzz
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 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 79764 46656
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Per MPI rank memory allocation (min/avg/max) = 96.44 | 96.44 | 96.44 Mbytes
Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
Loop time of 18.5289 on 1 procs for 100 steps with 18146 atoms
Performance: 0.466 ns/day, 51.469 hours/ns, 5.397 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.326 | 14.326 | 14.326 | 0.0 | 77.31
Bond | 0.65294 | 0.65294 | 0.65294 | 0.0 | 3.52
Kspace | 2.2291 | 2.2291 | 2.2291 | 0.0 | 12.03
Neigh | 1.2037 | 1.2037 | 1.2037 | 0.0 | 6.50
Comm | 0.038561 | 0.038561 | 0.038561 | 0.0 | 0.21
Output | 0.0022585 | 0.0022585 | 0.0022585 | 0.0 | 0.01
Modify | 0.058746 | 0.058746 | 0.058746 | 0.0 | 0.32
Other | | 0.018 | | | 0.10
Nlocal: 18146 ave 18146 max 18146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 29127 ave 29127 max 29127 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 441898 ave 441898 max 441898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 441898
Ave neighs/atom = 24.3524
Ave special neighs/atom = 5.92362
Neighbor list builds = 5
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:22

360
examples/USER/misc/momb/log.17Mar2017.system.g++.4 Normal file
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@ -0,0 +1,360 @@
LAMMPS (17 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# ----------------- 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 momb 12.0 0.75 20.0 morse 5.5
kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
read_data system.data
orthogonal box = (0 0 0) to (53.6198 53.6198 160)
1 by 1 by 4 MPI processor grid
reading atoms ...
18146 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
13 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
12694 bonds
reading angles ...
19786 angles
reading dihedrals ...
29690 dihedrals
reading impropers ...
5 impropers
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
23 = max # of special neighbors
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 momb 0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff 15 16 momb 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
minimize 1.0e-3 1.0e-5 1000 10000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 24276 11664
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 8 23
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/charmm/coul/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair momb, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) pair morse, perpetual, copy from (3)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 21.64 | 38.62 | 61.37 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10035.476 218.18376 -9817.2917 -1066.914
9 0 -10244.892 211.35072 -10033.541 -3283.8636
Loop time of 1.52429 on 4 procs for 9 steps with 18146 atoms
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9817.29174185 -10023.887559 -10033.5413886
Force two-norm initial, final = 76.9233 27.3547
Force max component initial, final = 11.8658 7.37882
Final line search alpha, max atom move = 0.0472944 0.348977
Iterations, force evaluations = 9 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13871 | 0.61412 | 1.3512 | 63.6 | 40.29
Bond | 0.0010097 | 0.021249 | 0.047945 | 13.0 | 1.39
Kspace | 0.11351 | 0.87771 | 1.3739 | 55.2 | 57.58
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0040638 | 0.0056078 | 0.0067704 | 1.6 | 0.37
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005606 | | | 0.37
Nlocal: 4536.5 ave 8000 max 700 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 11329.2 ave 16795 max 5072 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 109797 ave 237808 max 8314 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 439189
Ave neighs/atom = 24.2031
Ave special neighs/atom = 5.92362
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
velocity all create 413.0 12378 dist gaussian
thermo 10
thermo_style custom step pe ke etotal temp press pxx pyy pzz
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 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 24276 11664
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Per MPI rank memory allocation (min/avg/max) = 20.51 | 36.93 | 59.12 Mbytes
Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
Loop time of 10.6085 on 4 procs for 100 steps with 18146 atoms
Performance: 0.814 ns/day, 29.468 hours/ns, 9.426 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1362 | 3.9541 | 8.4741 | 152.5 | 37.27
Bond | 0.0070739 | 0.16051 | 0.36228 | 36.1 | 1.51
Kspace | 0.96032 | 5.5204 | 8.3734 | 130.4 | 52.04
Neigh | 0.70817 | 0.7087 | 0.70915 | 0.0 | 6.68
Comm | 0.061705 | 0.2165 | 0.40455 | 26.6 | 2.04
Output | 0.0013981 | 0.001441 | 0.0015171 | 0.1 | 0.01
Modify | 0.024801 | 0.030292 | 0.039353 | 3.1 | 0.29
Other | | 0.01646 | | | 0.16
Nlocal: 4536.5 ave 8016 max 572 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 11368.2 ave 16706 max 5173 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 110474 ave 236783 max 9217 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 441898
Ave neighs/atom = 24.3524
Ave special neighs/atom = 5.92362
Neighbor list builds = 5
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:12

80476
examples/USER/misc/momb/system.data Normal file
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File diff suppressed because it is too large Load Diff

2
src/.gitignore vendored
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@ -815,6 +815,8 @@
/pair_tri_lj.h
/pair_yukawa_colloid.cpp
/pair_yukawa_colloid.h
/pair_momb.cpp
/pair_momb.h
/pppm.cpp
/pppm.h
/pppm_cg.cpp

1
src/USER-MISC/README
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@ -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 momb, Kristen Fichthorn, Tonnam Balankura, Ya Zhou, fichthorn@psu.edu, 18 Mar 17
temper/grem, David Stelter, dstelter@bu.edu, 22 Nov 16

385
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@ -0,0 +1,385 @@
/* ----------------------------------------------------------------------
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, Tonnam Balankura, Ya Zhou @ Penn State University
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "pair_momb.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
using namespace LAMMPS_NS;
static const char cite_momb[] =
"Pair style momb:\n\n"
"@Article{pair_momb_2015,\n"
"title = {A force field for describing the polyvinylpyrrolidone-mediated"
" solution-phase synthesis of shape-selective Ag nanoparticles.},\n"
"volume = {118},\n"
"number = {6},\n"
"url = {http://dx.doi.org/10.1021/jp412098n},\n"
"doi = {10.1021/jp412098n},\n"
"journal = {J. Phys. Chem. C},\n"
"author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n"
"year = {2014},\n"
"pages = {3366--3374}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairMomb::PairMomb(LAMMPS *lmp) : Pair(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_momb);
}
/* ---------------------------------------------------------------------- */
PairMomb::~PairMomb()
{
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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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 PairMomb::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;
}

77
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@ -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, Tonnam Balankura, Ya Zhou @ Penn State University
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(momb,PairMomb)
#else
#ifndef LMP_PAIR_MOMB_H
#define LMP_PAIR_MOMB_H
#include "pair.h"
namespace LAMMPS_NS {
class PairMomb : public Pair {
public:
PairMomb(class LAMMPS *);
virtual ~PairMomb();
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.
*/