Merge https://github.com/lammps/lammps into pair_rann
This commit is contained in:
kipbarrett
36
examples/USER/misc/charge_regulation/README
Normal file
36
examples/USER/misc/charge_regulation/README
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@ -0,0 +1,36 @@
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This directory has two input scripts that illustrates how to use fix
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charge_regulation in LAMMPS to perform coarse-grained molecular dynamics
|
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(MD) simulations with incorporation of charge regulation effects. The
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charge regulation is implemented via Monte Carlo (MC) sampling following
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the reaction ensemble MC approach, producing a MC/MD hybrid tool for
|
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modeling charge regulation in solvated systems.
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|
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The script `in.chreg-acid` sets up a simple weak acid electrolyte
|
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(pH=7,pKa=6,pI=3). Four different types of MC moves are implemented:
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acid protonation & de-protonation, and monovalent ion pair insertion and
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deletion. Note here we have grouped all free monovalent ions into a
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single type, a physically natural choice on the level of coarse-grained
|
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primitive electrolyte models, which increases the calculation
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performance but has no effects on thermodynamic observables. The
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variables such as pH, pKa, pI, and lb at the top of the input script can
|
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be adjusted to play with various simulation parameters. The cumulative
|
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MC attempted moves and cumulative number of accepted moves, as well as,
|
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current number of neutral and charged acid particles, neutral and
|
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charged base particles (in this example always 0), and the current
|
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number of free cations and anions in the system are printed in the
|
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output.
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|
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The script `in.chreg-polymer` sets up a weak poly-electrolyte chain of
|
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N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7
|
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and monovalent salt chemical potential pI=3. In this example, we choose
|
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to treat salt ions, protons, and hydroxyl ions separately, which results
|
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in 5 types of MC moves: acid [type 1] protonation & de-protonation (with
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protons [type 4] insertion & deletion), acid [type 1] protonation &
|
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de-protonation (with salt cation [type 2] insertion & deletion), water
|
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self-ionization (insertion and deletion of proton [type4] and hydroxyl
|
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ion [type 5] pair), insertion and deletion of monovalent salt pair [type
|
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2 and type 3] , insertion and deletion of a proton [type4] and salt
|
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anion [type 3]. The current number of neutral and charged acid
|
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particles, the current number of free salt cations and anions, and the
|
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current number of protons and hydroxyl ions are printed in the output.
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235
examples/USER/misc/charge_regulation/data.chreg-acid
Normal file
235
examples/USER/misc/charge_regulation/data.chreg-acid
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@ -0,0 +1,235 @@
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LAMMPS data file generated by get_input.py
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219 atoms
|
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3 atom types
|
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-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi
|
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-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi
|
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-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi
|
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|
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Masses
|
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|
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1 1
|
||||
2 1
|
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3 1
|
||||
|
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Atoms
|
||||
|
||||
1 1 0 2.5983275747497636 -8.368052973860795 20.001288664343484
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
179 2 1 -9.048793002383698 -1.788614428205263 -11.841289777017172
|
||||
180 2 1 -22.49667217853208 -22.112076711777533 10.01393503943838
|
||||
181 2 1 -16.183333848138453 1.3098533508906556 0.8096413611556166
|
||||
182 2 1 -4.007575369376703 -24.447854073342157 -19.683971619997376
|
||||
183 2 1 8.79123015290173 -15.890906503248287 -23.45721570121758
|
||||
184 2 1 -8.557898021171628 -21.985380426316674 22.626382729361595
|
||||
185 2 1 7.143974673263372 16.57516065778192 0.5907315164854055
|
||||
186 2 1 7.05280226857041 6.658154377550723 17.993436860997946
|
||||
187 2 1 20.98391844656716 -3.7711929542825544 -22.37222924252256
|
||||
188 2 1 -8.856382807041598 -16.421301042649826 -7.682473719905396
|
||||
189 2 1 -14.381919492441797 -7.667674808763277 -10.178028203828621
|
||||
190 2 1 -22.93472549116592 10.072854607637751 3.756868463885592
|
||||
191 2 1 9.458987867260412 17.23200182595278 -0.03503381482496337
|
||||
192 2 1 11.013603635791974 19.842184408029837 -5.83598462187852
|
||||
193 2 1 23.28897987479008 2.835578651649044 -20.512845011389647
|
||||
194 2 1 -18.86161127148128 8.956542530565656 14.193388541103026
|
||||
195 2 1 13.688477473034126 -15.973205475346514 10.952445409682397
|
||||
196 2 1 2.1058159557459497 2.740725960214597 -23.72037436968614
|
||||
197 2 1 20.982351847235442 7.072739454450108 -24.07322254392252
|
||||
198 2 1 5.962360707177609 -19.424513569281604 22.469955103109243
|
||||
199 2 1 -17.13607356062674 20.038457022813326 12.94227215395123
|
||||
200 2 1 11.592617137491743 22.283887092702138 2.339699650677858
|
||||
201 2 1 -1.3864952037065237 19.199632510575505 -7.684210221911414
|
||||
202 2 1 -22.44476570586083 -19.66385674506424 -8.981660607669522
|
||||
203 2 1 0.36547911522815824 -7.628556098996082 16.326944822668068
|
||||
204 2 1 -9.766164330974753 24.38435844399602 -14.352553497163
|
||||
205 2 1 -0.6310792726759544 -5.625399375968325 13.665993163571486
|
||||
206 2 1 2.6795300975636103 -0.37097710463575595 15.575183407667495
|
||||
207 2 1 10.68508361399715 24.638181487800373 -17.538711281692827
|
||||
208 2 1 18.30809729940504 18.39121662193474 18.285926328751984
|
||||
209 2 1 -11.52561870836783 -11.871004571782223 12.890674390475048
|
||||
210 3 -1 16.038097437687007 -0.8308290507120688 9.140710202344948
|
||||
211 3 -1 -12.071581865552927 23.77532123232212 -6.250109721970887
|
||||
212 3 -1 24.179073767023887 19.6390206210449 22.20321951706368
|
||||
213 3 -1 22.899159789805424 8.918385700451317 -1.1269016129923664
|
||||
214 3 -1 -10.48576153865241 5.691510884812594 21.955276995406933
|
||||
215 3 -1 6.272776670877239 10.035821052072265 22.22030412319301
|
||||
216 3 -1 14.689947575936934 -7.785907120217196 0.5033983092114553
|
||||
217 3 -1 23.173937996535116 -21.041572031861037 -21.057283440516468
|
||||
218 3 -1 -6.015120142466472 6.3962924962024985 21.58241945230285
|
||||
219 3 -1 -0.77667042466472 0.3962848125024985 1.582473830285
|
||||
235
examples/USER/misc/charge_regulation/data.chreg-acid-real
Normal file
235
examples/USER/misc/charge_regulation/data.chreg-acid-real
Normal file
@ -0,0 +1,235 @@
|
||||
LAMMPS data file generated by get_input.py
|
||||
|
||||
219 atoms
|
||||
3 atom types
|
||||
-180 180 xlo xhi
|
||||
-180 180 ylo yhi
|
||||
-180 180 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 20
|
||||
2 20
|
||||
3 20
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 18.70795854 -60.24998141 144.0092784
|
||||
2 1 -1 -130.9166548 -58.17450505 59.42690807
|
||||
3 1 -1 -125.5489258 58.46696329 77.38308245
|
||||
4 1 -1 46.8178314 -169.1807517 143.6272062
|
||||
5 1 -1 -162.2028908 -135.2407217 -129.3455357
|
||||
6 1 -1 -69.93717134 136.6009615 -140.3684699
|
||||
7 1 -1 -92.39022725 0.88313303 -156.091658
|
||||
8 1 -1 150.5452585 -15.59052452 3.326246397
|
||||
9 1 -1 171.8072626 172.9794849 75.84528386
|
||||
10 1 -1 -3.808294794 171.5056017 -19.13183671
|
||||
11 1 -1 68.90552852 86.21187482 24.628687
|
||||
12 1 -1 -73.4512319 54.41387468 86.90435812
|
||||
13 1 -1 35.26889793 14.52239846 -149.5100547
|
||||
14 1 -1 -173.4235696 31.85993966 -30.27092231
|
||||
15 1 -1 26.52275652 -34.29527864 -91.86288894
|
||||
16 1 -1 -87.96846598 -127.5856503 -97.6057498
|
||||
17 1 -1 -154.4848498 -53.45277349 -49.99665917
|
||||
18 1 -1 98.62055171 61.22620607 58.21550969
|
||||
19 1 -1 -41.50240351 82.79211492 -36.80199381
|
||||
20 1 -1 28.75979595 121.8830702 -107.1045784
|
||||
21 1 -1 32.46858199 119.7785312 -159.9729476
|
||||
22 1 -1 159.2306995 -136.6051631 -172.6738992
|
||||
23 1 -1 102.0172393 -120.2283106 99.20908244
|
||||
24 1 -1 123.7452923 63.55770833 165.9991324
|
||||
25 1 -1 21.47248943 -121.2255157 -153.2060898
|
||||
26 1 -1 119.9343938 -11.67643844 -81.47418783
|
||||
27 1 -1 138.3518387 -111.6909718 52.34478391
|
||||
28 1 -1 -63.98455793 -173.4943975 28.8937153
|
||||
29 1 -1 151.1941205 32.1957053 2.770016951
|
||||
30 1 -1 9.678451862 40.32965827 -107.4138803
|
||||
31 1 -1 -50.13343476 147.3853225 -117.9277823
|
||||
32 1 -1 -71.89428479 68.56083346 -179.8533411
|
||||
33 1 -1 -124.7615264 41.48173515 41.18558752
|
||||
34 1 -1 37.21218965 -170.6314486 18.86382891
|
||||
35 1 -1 136.6419056 46.16558949 45.50222572
|
||||
36 1 -1 -117.9745136 -106.7487877 29.70172113
|
||||
37 1 -1 57.41607893 -135.959946 79.2519303
|
||||
38 1 -1 99.2146782 13.37903953 65.55038181
|
||||
39 1 -1 -172.1483566 -24.09752036 -73.64723741
|
||||
40 1 -1 155.6386288 60.79647905 -137.6687854
|
||||
41 1 -1 -63.53265172 104.1203088 115.6442718
|
||||
42 1 -1 -17.57295284 90.38545929 148.3687022
|
||||
43 1 -1 -132.9077114 109.8788504 152.5487953
|
||||
44 1 -1 16.09488244 -168.1200949 81.85901273
|
||||
45 1 -1 112.2904059 -47.57448978 39.12664557
|
||||
46 1 -1 -126.2033528 29.5901835 -10.20047838
|
||||
47 1 -1 15.56623544 -118.8796306 -87.74057744
|
||||
48 1 -1 -62.53683723 -50.93540139 -8.324528194
|
||||
49 1 -1 112.4826277 -47.2269151 148.0087872
|
||||
50 1 -1 -50.1494905 -103.3112513 -103.8344246
|
||||
51 1 -1 -87.11540287 -177.3205662 -114.041712
|
||||
52 1 -1 48.0517504 56.41745572 -69.94172272
|
||||
53 1 -1 -125.3768674 89.18463079 -121.5525657
|
||||
54 1 -1 157.6559442 89.89879164 -104.7846361
|
||||
55 1 -1 -60.30935405 -178.4439001 53.67216823
|
||||
56 1 -1 101.3842749 -156.3782696 -125.6200241
|
||||
57 1 -1 33.71034745 14.19807232 -56.33090362
|
||||
58 1 -1 31.34283781 114.2588441 177.621698
|
||||
59 1 -1 167.8681492 -33.73721495 17.70943601
|
||||
60 1 -1 50.73906277 165.7201913 -94.6041936
|
||||
61 1 -1 84.42400278 -113.8271268 -11.73087326
|
||||
62 1 -1 -146.6200007 -87.0115127 -164.2802459
|
||||
63 1 -1 -17.94345563 -5.266117623 -114.4770608
|
||||
64 1 -1 -161.6618755 -81.21577064 -68.78715057
|
||||
65 1 -1 178.3275787 144.9284223 75.80861878
|
||||
66 1 -1 81.54873843 -83.6941478 -69.75163018
|
||||
67 1 -1 -41.13190239 113.6079886 -6.669536125
|
||||
68 1 -1 -108.5270482 -89.08499627 -39.32427247
|
||||
69 1 -1 -41.97432027 -32.96246695 65.11935497
|
||||
70 1 -1 -39.09020679 10.47027922 -53.26049629
|
||||
71 1 -1 -168.3760012 -85.85704062 27.51501191
|
||||
72 1 -1 -7.699755475 21.59960856 26.43069039
|
||||
73 1 -1 87.36704757 14.21816794 -107.2504322
|
||||
74 1 -1 153.4284087 136.6052131 -126.1502487
|
||||
75 1 -1 -175.3682642 25.88313064 123.6455547
|
||||
76 1 -1 90.96648194 175.4891969 32.84622917
|
||||
77 1 -1 -77.3297511 139.285477 -24.02526586
|
||||
78 1 -1 -21.80051132 76.35556687 53.9496888
|
||||
79 1 -1 36.00388293 84.74463507 124.0379428
|
||||
80 1 -1 8.341344194 -176.0991953 -90.11296078
|
||||
81 1 -1 13.79742378 -101.263178 81.37760753
|
||||
82 1 -1 -150.1706978 153.3081009 125.261789
|
||||
83 1 -1 -176.434078 -91.73850736 -13.91415701
|
||||
84 1 -1 19.14212656 -8.014482902 53.93954558
|
||||
85 1 -1 -133.3111329 174.2862517 104.1616036
|
||||
86 1 -1 141.4028288 71.58712061 62.57853826
|
||||
87 1 -1 -55.41310448 84.69012271 -53.69230074
|
||||
88 1 -1 7.57030387 -82.51421069 121.7019339
|
||||
89 1 -1 6.593627122 170.3286085 -47.07783075
|
||||
90 1 -1 167.9772199 -52.51603119 -77.32359634
|
||||
91 1 -1 9.68753279 2.580696533 63.63273049
|
||||
92 1 -1 -157.900078 -78.41001295 -74.97298362
|
||||
93 1 -1 157.7779932 -77.61759639 83.11626672
|
||||
94 1 -1 8.735687555 -51.63741526 149.2886008
|
||||
95 1 -1 166.3370649 158.0395191 2.108272744
|
||||
96 1 -1 -136.2080224 -0.233620925 170.1641304
|
||||
97 1 -1 54.59763504 77.34086464 -34.97254442
|
||||
98 1 -1 -53.93524806 -102.0122253 -46.27109402
|
||||
99 1 -1 -148.8398471 -62.976886 79.28200649
|
||||
100 1 -1 -134.367229 -153.7685306 -62.89913905
|
||||
101 2 1 85.68701047 47.45902631 136.9309939
|
||||
102 2 1 -168.7218611 -136.4862888 34.82926874
|
||||
103 2 1 -85.14342147 -27.50852705 22.44064244
|
||||
104 2 1 -125.9841936 -166.432033 69.22175254
|
||||
105 2 1 78.40196016 32.48784706 134.5355212
|
||||
106 2 1 -158.7356866 172.6075363 -168.6081077
|
||||
107 2 1 -97.70696089 125.0552693 152.541151
|
||||
108 2 1 47.42532862 117.2059839 -26.2001494
|
||||
109 2 1 58.97843054 49.16794046 -45.70255405
|
||||
110 2 1 -113.2077086 -147.4896474 -109.0593944
|
||||
111 2 1 133.7818478 137.2370883 -74.12887346
|
||||
112 2 1 -151.8619681 -55.72321046 39.00697883
|
||||
113 2 1 -101.5491513 -113.5421107 -135.9492067
|
||||
114 2 1 -105.4410412 63.66017268 62.00391546
|
||||
115 2 1 -84.37716183 -35.78408568 -7.089644848
|
||||
116 2 1 140.387382 -75.00992841 -159.2710691
|
||||
117 2 1 157.3753205 145.1311104 -98.29723102
|
||||
118 2 1 -126.8885841 157.4914592 -47.04455377
|
||||
119 2 1 52.06885202 -100.2669325 38.59257737
|
||||
120 2 1 -54.06789629 137.7750035 -116.8953091
|
||||
121 2 1 -29.14739431 94.50860741 -51.527097
|
||||
122 2 1 -145.9322739 154.5384232 112.3421798
|
||||
123 2 1 -32.24342538 -22.90490626 -133.4101075
|
||||
124 2 1 155.0953371 97.30799449 -13.02231424
|
||||
125 2 1 -109.6079033 -42.89844953 -51.80376701
|
||||
126 2 1 -150.2770445 -55.20818421 147.7312972
|
||||
127 2 1 -26.96028917 151.3053234 51.82429115
|
||||
128 2 1 -42.51040448 55.12547194 -10.01649745
|
||||
129 2 1 -154.7332138 -166.4922488 75.56066422
|
||||
130 2 1 179.3252381 50.98353603 -103.842222
|
||||
131 2 1 -87.64561442 -167.4026399 -37.04977996
|
||||
132 2 1 -141.7543098 32.23109989 44.99445113
|
||||
133 2 1 121.3596596 -6.092779973 129.6856923
|
||||
134 2 1 124.4836766 -86.35531223 85.50625099
|
||||
135 2 1 140.6305506 -165.9843021 -35.3966949
|
||||
136 2 1 -89.51258901 36.2123163 54.25434215
|
||||
137 2 1 107.5306105 58.22419926 141.7457531
|
||||
138 2 1 -51.03564423 -166.277591 119.3103596
|
||||
139 2 1 106.3738063 153.673561 100.7747233
|
||||
140 2 1 -105.1662471 -49.88388187 -163.5658795
|
||||
141 2 1 -123.4063552 104.6405545 -157.1806703
|
||||
142 2 1 30.68517662 111.7365757 -128.0988407
|
||||
143 2 1 -70.66650991 -36.87088431 101.1920697
|
||||
144 2 1 59.85584345 28.56015074 -148.8751279
|
||||
145 2 1 76.34296857 -18.88899045 11.99663247
|
||||
146 2 1 -127.898772 9.029786744 -155.2067979
|
||||
147 2 1 -61.47407783 106.6906337 -32.24644961
|
||||
148 2 1 -41.82882356 105.2048819 95.67134776
|
||||
149 2 1 64.70518204 -125.5606981 -130.2221179
|
||||
150 2 1 -95.86998176 64.01110464 -62.69889224
|
||||
151 2 1 -3.893149866 -170.4938796 -173.9425756
|
||||
152 2 1 -142.5571999 -115.9852755 -42.33527796
|
||||
153 2 1 -170.1094774 67.22933296 -69.41406448
|
||||
154 2 1 -135.7002446 -117.3853245 -77.66219554
|
||||
155 2 1 97.68794466 -176.3481416 64.0577303
|
||||
156 2 1 98.30084322 -179.1048324 157.6098802
|
||||
157 2 1 -61.74657154 71.45180441 36.21267022
|
||||
158 2 1 148.9924395 8.130617629 2.580809806
|
||||
159 2 1 -7.179797893 131.8852645 48.92705878
|
||||
160 2 1 166.7210737 111.3028256 122.5151765
|
||||
161 2 1 160.4061661 105.4292149 147.9164951
|
||||
162 2 1 70.35573238 -156.217711 -37.86968306
|
||||
163 2 1 37.82167168 128.9612675 113.5371453
|
||||
164 2 1 -149.4650805 40.2544478 -89.16446826
|
||||
165 2 1 23.15794976 -35.62998186 -128.5225995
|
||||
166 2 1 148.5909499 65.59167763 44.47571026
|
||||
167 2 1 38.20567747 91.06090259 167.2556933
|
||||
168 2 1 -173.8935359 124.3001041 -123.4154022
|
||||
169 2 1 -113.0780192 -112.7185827 -75.51909042
|
||||
170 2 1 -47.52814398 -162.0232543 -40.84518679
|
||||
171 2 1 164.6580923 96.26106544 -67.52475023
|
||||
172 2 1 -166.687599 -28.28821753 -80.04284273
|
||||
173 2 1 9.786487166 -133.5748603 -110.4924395
|
||||
174 2 1 73.69685916 -130.6229707 -12.1566579
|
||||
175 2 1 90.69039384 -12.53964183 -156.8650452
|
||||
176 2 1 -1.065055548 123.2458955 9.207883208
|
||||
177 2 1 175.3144942 -62.38332615 89.50309521
|
||||
178 2 1 -135.5554643 -135.3786299 -12.22599884
|
||||
179 2 1 -65.15130962 -12.87802388 -85.25728639
|
||||
180 2 1 -161.9760397 -159.2069523 72.10033228
|
||||
181 2 1 -116.5200037 9.430944126 5.8294178
|
||||
182 2 1 -28.85454266 -176.0245493 -141.7245957
|
||||
183 2 1 63.2968571 -114.4145268 -168.891953
|
||||
184 2 1 -61.61686575 -158.2947391 162.9099557
|
||||
185 2 1 51.43661765 119.3411567 4.253266919
|
||||
186 2 1 50.78017633 47.93871152 129.5527454
|
||||
187 2 1 151.0842128 -27.15258927 -161.0800505
|
||||
188 2 1 -63.76595621 -118.2333675 -55.31381078
|
||||
189 2 1 -103.5498203 -55.20725862 -73.28180307
|
||||
190 2 1 -165.1300235 72.52455317 27.04945294
|
||||
191 2 1 68.10471264 124.0704131 -0.252243467
|
||||
192 2 1 79.29794618 142.8637277 -42.01908928
|
||||
193 2 1 167.6806551 20.41616629 -147.6924841
|
||||
194 2 1 -135.8036012 64.48710622 102.1923975
|
||||
195 2 1 98.55703781 -115.0070794 78.85760695
|
||||
196 2 1 15.16187488 19.73322691 -170.7866955
|
||||
197 2 1 151.0729333 50.92372407 -173.3272023
|
||||
198 2 1 42.92899709 -139.8564977 161.7836767
|
||||
199 2 1 -123.3797296 144.2768906 93.18435951
|
||||
200 2 1 83.46684339 160.4439871 16.84583748
|
||||
201 2 1 -9.982765467 138.2373541 -55.3263136
|
||||
202 2 1 -161.6023131 -141.5797686 -64.66795638
|
||||
203 2 1 2.63144963 -54.92560391 117.5540027
|
||||
204 2 1 -70.31638318 175.5673808 -103.3383852
|
||||
205 2 1 -4.543770763 -40.50287551 98.39515078
|
||||
206 2 1 19.2926167 -2.671035153 112.1413205
|
||||
207 2 1 76.93260202 177.3949067 -126.2787212
|
||||
208 2 1 131.8183006 132.4167597 131.6586696
|
||||
209 2 1 -82.9844547 -85.47123292 92.81285561
|
||||
210 3 -1 115.4743016 -5.981969165 65.81311346
|
||||
211 3 -1 -86.91538943 171.1823129 -45.00079
|
||||
212 3 -1 174.0893311 141.4009485 159.8631805
|
||||
213 3 -1 164.8739505 64.21237704 -8.113691614
|
||||
214 3 -1 -75.49748308 40.97887837 158.0779944
|
||||
215 3 -1 45.16399203 72.25791157 159.9861897
|
||||
216 3 -1 105.7676225 -56.05853127 3.624467826
|
||||
217 3 -1 166.8523536 -151.4993186 -151.6124408
|
||||
218 3 -1 -43.30886503 46.05330597 155.3934201
|
||||
219 3 -1 -5.592027058 2.85325065 11.39381158
|
||||
264
examples/USER/misc/charge_regulation/data.chreg-polymer
Normal file
264
examples/USER/misc/charge_regulation/data.chreg-polymer
Normal file
@ -0,0 +1,264 @@
|
||||
##A Weak PE Chain of N=80
|
||||
|
||||
160 atoms
|
||||
79 bonds
|
||||
|
||||
5 atom types
|
||||
1 bond types
|
||||
|
||||
-50 50 xlo xhi
|
||||
-50 50 ylo yhi
|
||||
-50 50 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
5 1.0
|
||||
|
||||
Atoms
|
||||
# atom_id molecule_id atom_type charge x y z
|
||||
1 1 1 -1 0 0 -48.37753795169063
|
||||
2 1 1 -1 0 0 -47.255075903381254
|
||||
3 1 1 -1 0 0 -46.13261385507188
|
||||
4 1 1 -1 0 0 -45.01015180676251
|
||||
5 1 1 -1 0 0 -43.887689758453135
|
||||
6 1 1 -1 0 0 -42.76522771014376
|
||||
7 1 1 -1 0 0 -41.64276566183439
|
||||
8 1 1 -1 0 0 -40.520303613525016
|
||||
9 1 1 -1 0 0 -39.39784156521564
|
||||
10 1 1 -1 0 0 -38.27537951690627
|
||||
11 1 1 -1 0 0 -37.1529174685969
|
||||
12 1 1 -1 0 0 -36.030455420287524
|
||||
13 1 1 -1 0 0 -34.90799337197815
|
||||
14 1 1 -1 0 0 -33.78553132366878
|
||||
15 1 1 -1 0 0 -32.663069275359405
|
||||
16 1 1 -1 0 0 -31.54060722705003
|
||||
17 1 1 -1 0 0 -30.41814517874066
|
||||
18 1 1 -1 0 0 -29.295683130431286
|
||||
19 1 1 -1 0 0 -28.173221082121913
|
||||
20 1 1 -1 0 0 -27.05075903381254
|
||||
21 1 1 -1 0 0 -25.928296985503167
|
||||
22 1 1 -1 0 0 -24.805834937193794
|
||||
23 1 1 -1 0 0 -23.68337288888442
|
||||
24 1 1 -1 0 0 -22.560910840575048
|
||||
25 1 1 -1 0 0 -21.438448792265675
|
||||
26 1 1 -1 0 0 -20.3159867439563
|
||||
27 1 1 -1 0 0 -19.19352469564693
|
||||
28 1 1 -1 0 0 -18.071062647337556
|
||||
29 1 1 -1 0 0 -16.948600599028183
|
||||
30 1 1 -1 0 0 -15.82613855071881
|
||||
31 1 1 -1 0 0 -14.703676502409436
|
||||
32 1 1 -1 0 0 -13.581214454100063
|
||||
33 1 1 -1 0 0 -12.45875240579069
|
||||
34 1 1 -1 0 0 -11.336290357481317
|
||||
35 1 1 -1 0 0 -10.213828309171944
|
||||
36 1 1 -1 0 0 -9.091366260862571
|
||||
37 1 1 -1 0 0 -7.968904212553198
|
||||
38 1 1 -1 0 0 -6.846442164243825
|
||||
39 1 1 -1 0 0 -5.723980115934452
|
||||
40 1 1 -1 0 0 -4.601518067625079
|
||||
41 1 1 -1 0 0 -3.4790560193157063
|
||||
42 1 1 -1 0 0 -2.3565939710063333
|
||||
43 1 1 -1 0 0 -1.2341319226969603
|
||||
44 1 1 -1 0 0 -0.11166987438758724
|
||||
45 1 1 -1 0 0 1.0107921739217858
|
||||
46 1 1 -1 0 0 2.133254222231159
|
||||
47 1 1 -1 0 0 3.255716270540532
|
||||
48 1 1 -1 0 0 4.378178318849905
|
||||
49 1 1 -1 0 0 5.500640367159278
|
||||
50 1 1 -1 0 0 6.623102415468651
|
||||
51 1 1 -1 0 0 7.745564463778024
|
||||
52 1 1 -1 0 0 8.868026512087397
|
||||
53 1 1 -1 0 0 9.99048856039677
|
||||
54 1 1 -1 0 0 11.112950608706143
|
||||
55 1 1 -1 0 0 12.235412657015516
|
||||
56 1 1 -1 0 0 13.357874705324889
|
||||
57 1 1 -1 0 0 14.480336753634262
|
||||
58 1 1 -1 0 0 15.602798801943635
|
||||
59 1 1 -1 0 0 16.725260850253008
|
||||
60 1 1 -1 0 0 17.84772289856238
|
||||
61 1 1 -1 0 0 18.970184946871754
|
||||
62 1 1 -1 0 0 20.092646995181127
|
||||
63 1 1 -1 0 0 21.2151090434905
|
||||
64 1 1 -1 0 0 22.337571091799873
|
||||
65 1 1 -1 0 0 23.460033140109246
|
||||
66 1 1 -1 0 0 24.58249518841862
|
||||
67 1 1 -1 0 0 25.704957236727992
|
||||
68 1 1 -1 0 0 26.827419285037365
|
||||
69 1 1 -1 0 0 27.949881333346738
|
||||
70 1 1 -1 0 0 29.07234338165611
|
||||
71 1 1 -1 0 0 30.194805429965484
|
||||
72 1 1 -1 0 0 31.317267478274857
|
||||
73 1 1 -1 0 0 32.43972952658423
|
||||
74 1 1 -1 0 0 33.5621915748936
|
||||
75 1 1 -1 0 0 34.684653623202976
|
||||
76 1 1 -1 0 0 35.80711567151235
|
||||
77 1 1 -1 0 0 36.92957771982172
|
||||
78 1 1 -1 0 0 38.052039768131095
|
||||
79 1 1 -1 0 0 39.17450181644047
|
||||
80 1 1 -1 0 0 40.29696386474984
|
||||
81 0 2 1 -27.886422274724097 27.72001798427955 38.68169635811057
|
||||
82 0 2 1 29.812255760623188 17.871838747003693 -29.094648426460257
|
||||
83 0 2 1 -13.23881351410531 13.28123966828678 -24.422176415560116
|
||||
84 0 2 1 4.9465650593939685 -37.7521903558826 -15.115417767729575
|
||||
85 0 2 1 34.82527943387106 29.457664434004897 -25.565595338061254
|
||||
86 0 2 1 46.35660570786446 -7.161776614070412 -20.2471250527001
|
||||
87 0 2 1 39.20854546781531 34.96815569014278 13.893531822586723
|
||||
88 0 2 1 -7.797240698180197 0.07861219105048889 48.686453603015224
|
||||
89 0 2 1 43.92391845355516 -39.42362941705827 22.448930565867585
|
||||
90 0 2 1 -40.371744364329984 -17.743039071967246 -15.08153047835009
|
||||
91 0 2 1 -21.573165497710058 -0.5844447399891948 -45.73596994149077
|
||||
92 0 2 1 -19.882394451769102 -7.392447895357577 30.733607063808876
|
||||
93 0 2 1 -17.393031309514107 26.882975097407467 -47.64059480000892
|
||||
94 0 2 1 25.652222561671735 1.0229206994719107 -14.959030208952043
|
||||
95 0 2 1 26.075045766879313 19.902341017250052 46.70284805469666
|
||||
96 0 2 1 39.91980369168496 0.753749460187592 -26.203575929573407
|
||||
97 0 2 1 13.777613371273958 7.112171629839359 -33.5270487721399
|
||||
98 0 2 1 18.944534687271826 20.090215089875286 -34.381335468790574
|
||||
99 0 2 1 -23.801856387842435 -42.275962146864586 -8.322936238250279
|
||||
100 0 2 1 -31.386991395893826 29.83894468611787 8.937114269513422
|
||||
101 0 2 1 -41.07090001085809 49.59339931450579 6.666864232174753
|
||||
102 0 2 1 -46.58911504232167 -32.46068937927039 19.40424197066872
|
||||
103 0 2 1 -39.94659416571965 -36.28203465180086 5.841020764632312
|
||||
104 0 2 1 -26.027467090120137 -41.05522015175137 -1.1145958296128313
|
||||
105 0 2 1 37.09602855959457 23.76087951027276 45.09142423198867
|
||||
106 0 2 1 -27.78138413517528 -48.97344929918942 45.91491289356401
|
||||
107 0 2 1 4.468912883622387 -5.217782298407556 6.381420595433383
|
||||
108 0 2 1 36.758686966564525 48.425582881586166 -25.909273336802997
|
||||
109 0 2 1 -27.045102667146036 -19.713951008254117 4.339232870380627
|
||||
110 0 2 1 -5.984280016624311 -49.45311479123866 36.35727783065221
|
||||
111 0 2 1 27.833389147163018 -47.80144978082761 -47.71458334276804
|
||||
112 0 2 1 -23.628507668044364 -30.353876765128685 36.174277933133254
|
||||
113 0 2 1 -40.93360714431151 40.1336490864843 -27.035347797435495
|
||||
114 0 2 1 6.3523980881104976 -28.636485436097082 -10.671354350535445
|
||||
115 0 2 1 42.765716958607086 -32.85779663523676 -1.9682360265562124
|
||||
116 0 2 1 -33.68069757415453 16.800769050458484 -6.273374390373085
|
||||
117 0 2 1 13.909148568042937 4.921040289518388 12.111069913598996
|
||||
118 0 2 1 6.728324076730296 -48.44092815223126 -35.92436883370601
|
||||
119 0 2 1 -18.121173967321912 -15.76903395165283 2.2495451015454933
|
||||
120 0 2 1 -11.75253233489407 -45.82569982175387 -12.477142440015896
|
||||
121 0 2 1 1.9713864197144133 17.961034900064007 32.97992150691711
|
||||
122 0 2 1 -3.993384770632943 -47.63120435620297 27.75490859098018
|
||||
123 0 2 1 -0.32208279553454844 -47.30616152402566 -22.751109302380367
|
||||
124 0 2 1 -0.135777029397957 23.88599790464609 -31.87440560354473
|
||||
125 0 2 1 -6.123924906817393 -2.038519565120424 45.4809181974626
|
||||
126 0 2 1 -29.622588299895046 42.40404115712096 6.640479709229595
|
||||
127 0 2 1 -11.694512971272673 19.983258641775762 -38.152427411711145
|
||||
128 0 2 1 -20.93721440637313 39.46397829322392 -45.52708262202337
|
||||
129 0 2 1 34.13340147809369 36.14268504987945 -23.978137043267044
|
||||
130 0 2 1 -37.422309952611485 29.181841318883087 27.55677757161692
|
||||
131 0 2 1 30.11314373799594 18.721794400471353 1.5553303682670574
|
||||
132 0 2 1 -7.3563467211571805 46.84253369205935 -39.84708490437832
|
||||
133 0 2 1 -3.695927445484358 2.494403998274727 -7.634369981832755
|
||||
134 0 2 1 44.09701173592077 17.717328437831043 31.54108326477207
|
||||
135 0 2 1 48.070189931616795 10.601166369398662 -28.28574863896286
|
||||
136 0 2 1 -7.044858382811761 -42.080663380241766 -1.4369925734636553
|
||||
137 0 2 1 -12.485032488076918 23.87106169116919 6.178803347562642
|
||||
138 0 2 1 -15.613232443702309 10.103630885941392 -20.447182948810916
|
||||
139 0 2 1 28.610332347774147 37.08335835592116 -19.90280831362493
|
||||
140 0 2 1 25.853920233242505 -27.768648181803655 24.971357611943475
|
||||
141 0 2 1 9.256159541363296 -23.562096053197934 -4.722701100419371
|
||||
142 0 2 1 39.96929397877305 -11.88228547846326 -28.70638149104603
|
||||
143 0 2 1 -37.98545134633291 -23.50528193202669 -10.939982626098441
|
||||
144 0 2 1 25.40017763114089 -47.49220127581256 15.1783064865064
|
||||
145 0 2 1 28.073596076651768 3.6631266774864386 31.54355751177208
|
||||
146 0 2 1 -19.596457173068703 46.79824882013442 -12.302655772327597
|
||||
147 0 2 1 -36.46192411958321 -2.785830672302666 -25.1901381125736
|
||||
148 0 2 1 -27.377389198969894 11.295792272951147 39.32842550184691
|
||||
149 0 2 1 32.24967019136358 -20.517755791016402 31.20590722085157
|
||||
150 0 2 1 47.70698618147787 9.75462874031868 -28.267447889542563
|
||||
151 0 2 1 17.157803106328345 -27.48141290657965 7.7670687016760525
|
||||
152 0 2 1 15.089833959419678 5.342811012118396 27.35336620165029
|
||||
153 0 2 1 9.836963929211372 -11.047378229392443 -20.960811370690678
|
||||
154 0 2 1 44.66600586278604 14.949733274456321 -29.328965994323575
|
||||
155 0 2 1 -21.006260382140685 8.492712712433658 -46.31580169190271
|
||||
156 0 2 1 -29.970979487850748 -36.46250489415931 26.914372830947457
|
||||
157 0 2 1 -1.0821372755756329 -8.453379951300242 -19.95665062432509
|
||||
158 0 2 1 -24.033653425909772 -39.51330620205049 20.067656167683793
|
||||
159 0 2 1 27.747287624384626 -21.904990435351312 -10.819345241055956
|
||||
160 0 2 1 -40.86737066410612 -25.609300376714796 -21.128139356809783
|
||||
|
||||
Bonds
|
||||
# bond_id bond_type atom1_id atom2_id
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 13 14
|
||||
14 1 14 15
|
||||
15 1 15 16
|
||||
16 1 16 17
|
||||
17 1 17 18
|
||||
18 1 18 19
|
||||
19 1 19 20
|
||||
20 1 20 21
|
||||
21 1 21 22
|
||||
22 1 22 23
|
||||
23 1 23 24
|
||||
24 1 24 25
|
||||
25 1 25 26
|
||||
26 1 26 27
|
||||
27 1 27 28
|
||||
28 1 28 29
|
||||
29 1 29 30
|
||||
30 1 30 31
|
||||
31 1 31 32
|
||||
32 1 32 33
|
||||
33 1 33 34
|
||||
34 1 34 35
|
||||
35 1 35 36
|
||||
36 1 36 37
|
||||
37 1 37 38
|
||||
38 1 38 39
|
||||
39 1 39 40
|
||||
40 1 40 41
|
||||
41 1 41 42
|
||||
42 1 42 43
|
||||
43 1 43 44
|
||||
44 1 44 45
|
||||
45 1 45 46
|
||||
46 1 46 47
|
||||
47 1 47 48
|
||||
48 1 48 49
|
||||
49 1 49 50
|
||||
50 1 50 51
|
||||
51 1 51 52
|
||||
52 1 52 53
|
||||
53 1 53 54
|
||||
54 1 54 55
|
||||
55 1 55 56
|
||||
56 1 56 57
|
||||
57 1 57 58
|
||||
58 1 58 59
|
||||
59 1 59 60
|
||||
60 1 60 61
|
||||
61 1 61 62
|
||||
62 1 62 63
|
||||
63 1 63 64
|
||||
64 1 64 65
|
||||
65 1 65 66
|
||||
66 1 66 67
|
||||
67 1 67 68
|
||||
68 1 68 69
|
||||
69 1 69 70
|
||||
70 1 70 71
|
||||
71 1 71 72
|
||||
72 1 72 73
|
||||
73 1 73 74
|
||||
74 1 74 75
|
||||
75 1 75 76
|
||||
76 1 76 77
|
||||
77 1 77 78
|
||||
78 1 78 79
|
||||
79 1 79 80
|
||||
36
examples/USER/misc/charge_regulation/in.chreg-acid
Normal file
36
examples/USER/misc/charge_regulation/in.chreg-acid
Normal file
@ -0,0 +1,36 @@
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-acid
|
||||
|
||||
variable cut_long equal 12.5
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)
|
||||
variable lunit_nm equal 0.72 # in the units of nm
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_coeff * * 1.0 1.0
|
||||
kspace_style ewald 1.0e-3
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep 0.005
|
||||
run 2000
|
||||
44
examples/USER/misc/charge_regulation/in.chreg-acid-real
Normal file
44
examples/USER/misc/charge_regulation/in.chreg-acid-real
Normal file
@ -0,0 +1,44 @@
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
neighbor 10.0 bin
|
||||
read_data data.chreg-acid-real
|
||||
|
||||
#real units
|
||||
variable sigma equal 7.2 # particle diameter 0.72 nm
|
||||
variable temperature equal 298 # temperature 298 K
|
||||
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
||||
variable epsilon equal ${kb}*${temperature}
|
||||
variable tunit equal 2000 # time unit is 2000 fs
|
||||
variable timestep equal 0.005*${tunit}
|
||||
|
||||
variable cut_long equal 12.5*${sigma}
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)*${sigma}
|
||||
velocity all create ${temperature} 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_coeff * * ${epsilon} ${sigma}
|
||||
kspace_style pppm 1.0e-3
|
||||
dielectric 78
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep ${timestep}
|
||||
run 2000
|
||||
33
examples/USER/misc/charge_regulation/in.chreg-polymer
Normal file
33
examples/USER/misc/charge_regulation/in.chreg-polymer
Normal file
@ -0,0 +1,33 @@
|
||||
# Charge regulation lammps for a polymer chain
|
||||
units lj
|
||||
atom_style full
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-polymer
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 100 1.122462 # K R0
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long 1.122462 20
|
||||
pair_coeff * * 1.0 1.0 1.122462 # charges
|
||||
kspace_style pppm 1.0e-3
|
||||
pair_modify shift yes
|
||||
dielectric 1.0
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
|
||||
fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
|
||||
fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
|
||||
|
||||
thermo 100
|
||||
# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
|
||||
thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
|
||||
timestep 0.005
|
||||
run 2000
|
||||
@ -0,0 +1,125 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-acid
|
||||
Reading data file ...
|
||||
orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
variable cut_long equal 12.5
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)
|
||||
variable lunit_nm equal 0.72 # in the units of nm
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_style lj/cut/coul/long 1.12246204830937 ${cut_long}
|
||||
pair_style lj/cut/coul/long 1.12246204830937 12.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
kspace_style ewald 1.0e-3
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep 0.005
|
||||
run 2000
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.14221027
|
||||
estimated absolute RMS force accuracy = 0.0010128126
|
||||
estimated relative force accuracy = 0.0010128126
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 15.5
|
||||
ghost atom cutoff = 15.5
|
||||
binsize = 7.75, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes
|
||||
Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
0 -0.049662059 1 0 0 1 99 0 0 109 10
|
||||
100 -0.053672881 0.99159291 100 71 16 84 0 0 92 8
|
||||
200 -0.053383027 0.90935145 200 156 26 74 0 0 85 11
|
||||
300 -0.040471335 0.97937429 300 240 21 79 0 0 87 8
|
||||
400 -0.036188123 1.0837424 400 319 14 86 0 0 92 6
|
||||
500 -0.057294925 1.0507526 500 407 10 90 0 0 98 8
|
||||
600 -0.056009748 1.0669354 600 487 15 85 0 0 92 7
|
||||
700 -0.069686562 0.99202496 700 567 14 86 0 0 96 10
|
||||
800 -0.054695624 1.0592933 800 647 25 75 0 0 82 7
|
||||
900 -0.058693653 0.97870458 900 728 27 73 0 0 83 10
|
||||
1000 -0.062352957 1.0008923 1000 805 24 76 0 0 84 8
|
||||
1100 -0.065011926 0.91691048 1100 886 22 78 0 0 87 9
|
||||
1200 -0.080463686 0.98879304 1200 963 23 77 0 0 88 11
|
||||
1300 -0.062146141 1.0566033 1300 1047 21 79 0 0 88 9
|
||||
1400 -0.046980246 1.0847512 1400 1129 17 83 0 0 94 11
|
||||
1500 -0.042935292 1.0075805 1500 1203 24 76 0 0 86 10
|
||||
1600 -0.056075891 0.94173489 1600 1277 23 77 0 0 90 13
|
||||
1700 -0.042279161 1.1126317 1700 1355 28 72 0 0 82 10
|
||||
1800 -0.036842528 1.0255327 1800 1436 24 76 0 0 83 7
|
||||
1900 -0.038816022 0.93883373 1900 1511 23 77 0 0 86 9
|
||||
2000 -0.047008287 0.98904085 2000 1592 26 74 0 0 81 7
|
||||
Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms
|
||||
|
||||
Performance: 74249.079 tau/day, 171.873 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24337 | 0.24337 | 0.24337 | 0.0 | 2.09
|
||||
Kspace | 4.6009 | 4.6009 | 4.6009 | 0.0 | 39.54
|
||||
Neigh | 0.023451 | 0.023451 | 0.023451 | 0.0 | 0.20
|
||||
Comm | 0.027729 | 0.027729 | 0.027729 | 0.0 | 0.24
|
||||
Output | 0.0007813 | 0.0007813 | 0.0007813 | 0.0 | 0.01
|
||||
Modify | 6.7345 | 6.7345 | 6.7345 | 0.0 | 57.87
|
||||
Other | | 0.005713 | | | 0.05
|
||||
|
||||
Nlocal: 188.000 ave 188 max 188 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 597.000 ave 597 max 597 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2196.00 ave 2196 max 2196 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2196
|
||||
Ave neighs/atom = 11.680851
|
||||
Neighbor list builds = 2059
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
@ -0,0 +1,125 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-acid
|
||||
Reading data file ...
|
||||
orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
variable cut_long equal 12.5
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)
|
||||
variable lunit_nm equal 0.72 # in the units of nm
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_style lj/cut/coul/long 1.12246204830937 ${cut_long}
|
||||
pair_style lj/cut/coul/long 1.12246204830937 12.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
kspace_style ewald 1.0e-3
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep 0.005
|
||||
run 2000
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.14221027
|
||||
estimated absolute RMS force accuracy = 0.0010128126
|
||||
estimated relative force accuracy = 0.0010128126
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 15.5
|
||||
ghost atom cutoff = 15.5
|
||||
binsize = 7.75, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
|
||||
Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
0 -0.049662059 1 0 0 1 99 0 0 109 10
|
||||
100 -0.06196414 1.0156327 100 72 15 85 0 0 93 8
|
||||
200 -0.053901683 0.95128403 200 160 24 76 0 0 87 11
|
||||
300 -0.043852423 0.98035058 300 246 22 78 0 0 85 7
|
||||
400 -0.048370798 1.0909844 400 324 16 84 0 0 91 7
|
||||
500 -0.042546472 1.026849 500 410 13 87 0 0 95 8
|
||||
600 -0.06133022 0.97805065 600 494 14 86 0 0 93 7
|
||||
700 -0.053815853 1.0641005 700 572 17 83 0 0 91 8
|
||||
800 -0.059974814 1.0192348 800 650 23 77 0 0 83 6
|
||||
900 -0.051808132 1.0773288 900 728 25 75 0 0 85 10
|
||||
1000 -0.050390995 1.0236954 1000 804 28 72 0 0 81 9
|
||||
1100 -0.069766444 1.030965 1100 890 25 75 0 0 85 10
|
||||
1200 -0.074580231 1.0490058 1200 963 21 79 0 0 88 9
|
||||
1300 -0.060169443 0.93456607 1300 1043 22 78 0 0 86 8
|
||||
1400 -0.05120764 1.0374062 1400 1127 19 81 0 0 92 11
|
||||
1500 -0.027644416 0.99804782 1500 1204 24 76 0 0 85 9
|
||||
1600 -0.038599195 0.99015524 1600 1283 22 78 0 0 90 12
|
||||
1700 -0.050222686 1.1444379 1700 1365 27 73 0 0 84 11
|
||||
1800 -0.049338003 1.1188048 1800 1449 22 78 0 0 84 6
|
||||
1900 -0.04533154 0.99894341 1900 1527 22 78 0 0 86 8
|
||||
2000 -0.058837311 0.95302017 2000 1608 26 74 0 0 81 7
|
||||
Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms
|
||||
|
||||
Performance: 217020.495 tau/day, 502.362 timesteps/s
|
||||
96.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.050626 | 0.061127 | 0.071318 | 3.4 | 1.54
|
||||
Kspace | 1.1987 | 1.2504 | 1.288 | 3.1 | 31.41
|
||||
Neigh | 0.0056982 | 0.0063858 | 0.0069821 | 0.7 | 0.16
|
||||
Comm | 0.068302 | 0.11638 | 0.17922 | 12.8 | 2.92
|
||||
Output | 0.00055408 | 0.00092399 | 0.0020106 | 0.0 | 0.02
|
||||
Modify | 2.5399 | 2.5406 | 2.5417 | 0.0 | 63.81
|
||||
Other | | 0.005394 | | | 0.14
|
||||
|
||||
Nlocal: 47.0000 ave 55 max 42 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Nghost: 328.250 ave 335 max 317 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 547.000 ave 659 max 466 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2188
|
||||
Ave neighs/atom = 11.638298
|
||||
Neighbor list builds = 2057
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
@ -0,0 +1,131 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Charge regulation lammps for a polymer chain
|
||||
units lj
|
||||
atom_style full
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-polymer
|
||||
Reading data file ...
|
||||
orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
160 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
79 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 100 1.122462 # K R0
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long 1.122462 20
|
||||
pair_coeff * * 1.0 1.0 1.122462 # charges
|
||||
kspace_style pppm 1.0e-3
|
||||
pair_modify shift yes
|
||||
dielectric 1.0
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
|
||||
fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
|
||||
fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
|
||||
|
||||
thermo 100
|
||||
# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
|
||||
thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
|
||||
timestep 0.005
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.077106934
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00074388331
|
||||
estimated relative force accuracy = 0.00074388331
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2197 512
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg1
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg2
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg3
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 23
|
||||
ghost atom cutoff = 23
|
||||
binsize = 11.5, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, 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) = 6.962 | 6.962 | 6.962 Mbytes
|
||||
Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
0 0.50528297 1 0 80 80 0 0 0
|
||||
100 0.61185377 0.95892928 13 67 74 7 0 0
|
||||
200 0.54355177 1.1282424 19 61 76 15 0 0
|
||||
300 0.4519957 1.0764688 20 60 85 26 1 0
|
||||
400 0.41479389 0.99212685 24 56 92 36 0 0
|
||||
500 0.37382446 0.99776674 28 52 98 46 0 0
|
||||
600 0.34785337 1.1115081 28 52 109 57 0 0
|
||||
700 0.34637618 1.0332262 28 52 120 68 0 0
|
||||
800 0.21020932 1.1264036 29 51 125 74 0 0
|
||||
900 0.21246108 1.1168609 30 50 131 81 0 0
|
||||
1000 0.20997475 1.1201478 32 48 132 84 0 0
|
||||
1100 0.1984165 1.0209092 31 49 144 95 0 0
|
||||
1200 0.2061932 0.95880059 35 45 151 106 0 0
|
||||
1300 0.17220376 0.980077 36 44 156 112 0 0
|
||||
1400 0.15671143 0.93535342 37 43 161 118 0 0
|
||||
1500 0.16174665 0.9495928 36 44 168 124 0 0
|
||||
1600 0.11062965 0.94072924 40 40 164 124 0 0
|
||||
1700 0.13002563 0.95010828 38 42 167 125 0 0
|
||||
1800 0.14527814 0.93555342 37 43 172 129 0 0
|
||||
1900 0.17627465 0.96682495 32 48 176 128 0 0
|
||||
2000 0.16497265 0.95226954 33 47 180 133 0 0
|
||||
Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms
|
||||
|
||||
Performance: 115895.577 tau/day, 268.277 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.45607 | 0.45607 | 0.45607 | 0.0 | 6.12
|
||||
Bond | 0.0062385 | 0.0062385 | 0.0062385 | 0.0 | 0.08
|
||||
Kspace | 2.3257 | 2.3257 | 2.3257 | 0.0 | 31.20
|
||||
Neigh | 0.067103 | 0.067103 | 0.067103 | 0.0 | 0.90
|
||||
Comm | 0.02577 | 0.02577 | 0.02577 | 0.0 | 0.35
|
||||
Output | 0.00087047 | 0.00087047 | 0.00087047 | 0.0 | 0.01
|
||||
Modify | 4.5664 | 4.5664 | 4.5664 | 0.0 | 61.25
|
||||
Other | | 0.006848 | | | 0.09
|
||||
|
||||
Nlocal: 393.000 ave 393 max 393 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 749.000 ave 749 max 749 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5359.00 ave 5359 max 5359 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5359
|
||||
Ave neighs/atom = 13.636132
|
||||
Ave special neighs/atom = 1.1908397
|
||||
Neighbor list builds = 1489
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -0,0 +1,131 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Charge regulation lammps for a polymer chain
|
||||
units lj
|
||||
atom_style full
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-polymer
|
||||
Reading data file ...
|
||||
orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
160 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
79 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.016 seconds
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 100 1.122462 # K R0
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long 1.122462 20
|
||||
pair_coeff * * 1.0 1.0 1.122462 # charges
|
||||
kspace_style pppm 1.0e-3
|
||||
pair_modify shift yes
|
||||
dielectric 1.0
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
|
||||
fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
|
||||
fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
|
||||
|
||||
thermo 100
|
||||
# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
|
||||
thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
|
||||
timestep 0.005
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.077106934
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00074388331
|
||||
estimated relative force accuracy = 0.00074388331
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 1053 128
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg1
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg2
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg3
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 23
|
||||
ghost atom cutoff = 23
|
||||
binsize = 11.5, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, 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) = 6.878 | 6.935 | 6.992 Mbytes
|
||||
Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
0 0.50528297 1 0 80 80 0 0 0
|
||||
100 0.60223729 0.89547569 13 67 75 8 0 0
|
||||
200 0.65253636 0.87662399 18 62 78 16 0 0
|
||||
300 0.51550501 1.0542131 22 58 84 27 1 0
|
||||
400 0.43566766 0.94557633 26 54 90 36 0 0
|
||||
500 0.36269507 1.0386276 31 49 94 45 0 0
|
||||
600 0.32430641 0.99903033 27 53 111 58 0 0
|
||||
700 0.30255299 0.91225991 28 52 121 69 0 0
|
||||
800 0.27189951 0.9747089 28 52 127 75 0 0
|
||||
900 0.25495247 1.0747821 28 52 135 83 0 0
|
||||
1000 0.25950416 0.95256449 32 48 134 86 0 0
|
||||
1100 0.22561248 1.0102255 32 48 147 99 0 0
|
||||
1200 0.1734754 0.99475154 33 47 157 110 0 0
|
||||
1300 0.20081084 0.99873599 36 44 160 116 0 0
|
||||
1400 0.14240417 0.99442152 36 44 164 121 1 0
|
||||
1500 0.15314186 0.94559876 39 41 167 126 0 0
|
||||
1600 0.13574107 1.0484195 43 37 164 127 0 0
|
||||
1700 0.14477789 1.0105172 42 38 166 128 0 0
|
||||
1800 0.13493107 1.0349667 41 39 171 132 0 0
|
||||
1900 0.14849779 0.9994329 33 47 178 131 0 0
|
||||
2000 0.14485171 0.99739608 34 46 183 137 0 0
|
||||
Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms
|
||||
|
||||
Performance: 270955.695 tau/day, 627.212 timesteps/s
|
||||
94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.086456 | 0.11738 | 0.18562 | 11.8 | 3.68
|
||||
Bond | 0.00099182 | 0.0018544 | 0.0030079 | 1.8 | 0.06
|
||||
Kspace | 0.77406 | 0.79354 | 0.80895 | 1.5 | 24.89
|
||||
Neigh | 0.017894 | 0.017948 | 0.018002 | 0.0 | 0.56
|
||||
Comm | 0.029044 | 0.07885 | 0.11432 | 11.3 | 2.47
|
||||
Output | 0.00054932 | 0.0009656 | 0.0021319 | 0.0 | 0.03
|
||||
Modify | 2.1676 | 2.1706 | 2.1733 | 0.2 | 68.07
|
||||
Other | | 0.007591 | | | 0.24
|
||||
|
||||
Nlocal: 100.000 ave 110 max 89 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 415.000 ave 418 max 411 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 1360.75 ave 1872 max 1018 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 5443
|
||||
Ave neighs/atom = 13.607500
|
||||
Ave special neighs/atom = 1.1700000
|
||||
Neighbor list builds = 1492
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
neighbor 10.0 bin
|
||||
read_data data.chreg-acid-real
|
||||
Reading data file ...
|
||||
orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
#real units
|
||||
variable sigma equal 7.2 # particle diameter 0.72 nm
|
||||
variable temperature equal 298 # temperature 298 K
|
||||
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
||||
variable epsilon equal ${kb}*${temperature}
|
||||
variable epsilon equal 0.0019872067*${temperature}
|
||||
variable epsilon equal 0.0019872067*298
|
||||
variable tunit equal 2000 # time unit is 2000 fs
|
||||
variable timestep equal 0.005*${tunit}
|
||||
variable timestep equal 0.005*2000
|
||||
|
||||
variable cut_long equal 12.5*${sigma}
|
||||
variable cut_long equal 12.5*7.2
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)*${sigma}
|
||||
variable cut_lj equal 2^(1.0/6.0)*7.2
|
||||
velocity all create ${temperature} 8008 loop geom
|
||||
velocity all create 298 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 90
|
||||
pair_coeff * * ${epsilon} ${sigma}
|
||||
pair_coeff * * 0.5921875966 ${sigma}
|
||||
pair_coeff * * 0.5921875966 7.2
|
||||
kspace_style pppm 1.0e-3
|
||||
dielectric 78
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 298 $(v_tunit) 123
|
||||
fix fT all langevin 298 298 2000 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep ${timestep}
|
||||
timestep 10
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.019408615
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00012527706
|
||||
estimated relative force accuracy = 3.7726815e-07
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 2197 512
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 100
|
||||
ghost atom cutoff = 100
|
||||
binsize = 50, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.708 | 3.708 | 3.708 Mbytes
|
||||
Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
0 -6.4798431 298 0 0 1 99 0 0 109 10
|
||||
100 -6.9219668 306.44177 100 77 15 85 0 0 94 9
|
||||
200 -6.8175255 306.64254 200 164 23 77 0 0 87 10
|
||||
300 -5.2482381 331.67831 300 248 21 79 0 0 85 6
|
||||
400 -7.4531538 285.3495 400 326 17 83 0 0 89 6
|
||||
500 -6.9662528 286.2123 500 408 14 86 0 0 95 9
|
||||
600 -6.528214 291.41762 600 492 14 86 0 0 95 9
|
||||
700 -6.290871 271.50948 700 567 14 86 0 0 96 10
|
||||
800 -6.4944741 300.66261 800 650 23 77 0 0 83 6
|
||||
900 -8.0414672 305.6179 900 731 25 75 0 0 84 9
|
||||
1000 -8.5694583 298.73349 1000 810 25 75 0 0 83 8
|
||||
1100 -8.6677368 269.67435 1100 894 22 78 0 0 87 9
|
||||
1200 -8.2246183 284.14886 1200 969 22 78 0 0 88 10
|
||||
1300 -7.7674621 320.04838 1300 1040 23 77 0 0 85 8
|
||||
1400 -9.5186335 303.48091 1400 1124 18 82 0 0 93 11
|
||||
1500 -5.8437493 271.40712 1500 1204 25 75 0 0 83 8
|
||||
1600 -5.9149181 268.24708 1600 1285 23 77 0 0 90 13
|
||||
1700 -6.5047738 303.79732 1700 1369 27 73 0 0 84 11
|
||||
1800 -7.3010139 308.98213 1800 1450 22 78 0 0 83 5
|
||||
1900 -6.3505397 306.94357 1900 1527 22 78 0 0 86 8
|
||||
2000 -5.7144173 287.06184 2000 1605 27 73 0 0 80 7
|
||||
Loop time of 1.17189 on 1 procs for 2000 steps with 187 atoms
|
||||
|
||||
Performance: 1474.535 ns/day, 0.016 hours/ns, 1706.638 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.035807 | 0.035807 | 0.035807 | 0.0 | 3.06
|
||||
Kspace | 0.37689 | 0.37689 | 0.37689 | 0.0 | 32.16
|
||||
Neigh | 0.008694 | 0.008694 | 0.008694 | 0.0 | 0.74
|
||||
Comm | 0.004793 | 0.004793 | 0.004793 | 0.0 | 0.41
|
||||
Output | 0.000746 | 0.000746 | 0.000746 | 0.0 | 0.06
|
||||
Modify | 0.74292 | 0.74292 | 0.74292 | 0.0 | 63.39
|
||||
Other | | 0.00205 | | | 0.17
|
||||
|
||||
Nlocal: 187.000 ave 187 max 187 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 437.000 ave 437 max 437 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1500.00 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1500
|
||||
Ave neighs/atom = 8.0213904
|
||||
Neighbor list builds = 2080
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
neighbor 10.0 bin
|
||||
read_data data.chreg-acid-real
|
||||
Reading data file ...
|
||||
orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
#real units
|
||||
variable sigma equal 7.2 # particle diameter 0.72 nm
|
||||
variable temperature equal 298 # temperature 298 K
|
||||
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
||||
variable epsilon equal ${kb}*${temperature}
|
||||
variable epsilon equal 0.0019872067*${temperature}
|
||||
variable epsilon equal 0.0019872067*298
|
||||
variable tunit equal 2000 # time unit is 2000 fs
|
||||
variable timestep equal 0.005*${tunit}
|
||||
variable timestep equal 0.005*2000
|
||||
|
||||
variable cut_long equal 12.5*${sigma}
|
||||
variable cut_long equal 12.5*7.2
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)*${sigma}
|
||||
variable cut_lj equal 2^(1.0/6.0)*7.2
|
||||
velocity all create ${temperature} 8008 loop geom
|
||||
velocity all create 298 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 90
|
||||
pair_coeff * * ${epsilon} ${sigma}
|
||||
pair_coeff * * 0.5921875966 ${sigma}
|
||||
pair_coeff * * 0.5921875966 7.2
|
||||
kspace_style pppm 1.0e-3
|
||||
dielectric 78
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 298 $(v_tunit) 123
|
||||
fix fT all langevin 298 298 2000 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep ${timestep}
|
||||
timestep 10
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.019408615
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00012527706
|
||||
estimated relative force accuracy = 3.7726815e-07
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 1053 128
|
||||
0 atoms in group FixChargeRegulation:exclusion_group:chareg
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 100
|
||||
ghost atom cutoff = 100
|
||||
binsize = 50, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes
|
||||
Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
0 -6.4798431 298 0 0 1 99 0 0 109 10
|
||||
100 -7.6327126 304.68909 100 73 15 85 0 0 94 9
|
||||
200 -6.1699041 272.19597 200 156 24 76 0 0 87 11
|
||||
300 -7.7876571 288.90801 300 240 20 80 0 0 87 7
|
||||
400 -6.3239918 274.65708 400 315 16 84 0 0 90 6
|
||||
500 -5.3978659 257.49208 500 398 15 85 0 0 93 8
|
||||
600 -5.6433949 322.52048 600 477 18 82 0 0 90 8
|
||||
700 -6.5351367 269.20244 700 558 18 82 0 0 91 9
|
||||
800 -6.2093085 315.21326 800 638 24 76 0 0 83 7
|
||||
900 -7.0795998 311.93228 900 719 28 72 0 0 82 10
|
||||
1000 -6.4668438 281.72674 1000 796 27 73 0 0 81 8
|
||||
1100 -6.2377994 318.48594 1100 875 25 75 0 0 84 9
|
||||
1200 -6.6305072 304.9091 1200 950 23 77 0 0 87 10
|
||||
1300 -5.9624552 286.05027 1300 1029 22 78 0 0 86 8
|
||||
1400 -4.4695814 261.81053 1400 1111 20 80 0 0 90 10
|
||||
1500 -5.6928652 293.72403 1500 1191 24 76 0 0 86 10
|
||||
1600 -6.8715413 290.47065 1600 1275 22 78 0 0 90 12
|
||||
1700 -6.5067505 292.74735 1700 1356 25 75 0 0 85 10
|
||||
1800 -5.3902702 307.79012 1800 1434 22 78 0 0 83 5
|
||||
1900 -5.1407153 318.48918 1900 1510 21 79 0 0 87 8
|
||||
2000 -4.9514719 281.87771 2000 1589 25 75 0 0 82 7
|
||||
Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms
|
||||
|
||||
Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.008399 | 0.010383 | 0.011765 | 1.2 | 1.84
|
||||
Kspace | 0.17501 | 0.17543 | 0.1757 | 0.1 | 31.17
|
||||
Neigh | 0.001833 | 0.0021325 | 0.002293 | 0.4 | 0.38
|
||||
Comm | 0.023099 | 0.024255 | 0.026645 | 0.9 | 4.31
|
||||
Output | 0.000465 | 0.000546 | 0.000783 | 0.0 | 0.10
|
||||
Modify | 0.3464 | 0.34669 | 0.34698 | 0.0 | 61.59
|
||||
Other | | 0.003452 | | | 0.61
|
||||
|
||||
Nlocal: 47.2500 ave 57 max 41 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 285.750 ave 303 max 263 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 403.500 ave 548 max 324 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1614
|
||||
Ave neighs/atom = 8.5396825
|
||||
Neighbor list builds = 2081
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
1
examples/USER/pace/Cu-PBE-core-rep.ace
Symbolic link
1
examples/USER/pace/Cu-PBE-core-rep.ace
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Cu-PBE-core-rep.ace
|
||||
38
examples/USER/pace/in.pace.product
Normal file
38
examples/USER/pace/in.pace.product
Normal file
@ -0,0 +1,38 @@
|
||||
# simple test of fcc Cu with ACE product
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 10 check yes
|
||||
|
||||
variable a equal 3.597
|
||||
lattice fcc $a
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
|
||||
pair_style pace product
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
|
||||
velocity all create 300 8728 loop geom
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
variable delenergy equal c_energy-pe
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||
|
||||
run 100
|
||||
|
||||
38
examples/USER/pace/in.pace.recursive
Normal file
38
examples/USER/pace/in.pace.recursive
Normal file
@ -0,0 +1,38 @@
|
||||
# simple test of fcc Cu with ACE recursive
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 10 check yes
|
||||
|
||||
variable a equal 3.597
|
||||
lattice fcc $a
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
|
||||
pair_style pace recursive
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
|
||||
velocity all create 300 8728 loop geom
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
variable delenergy equal c_energy-pe
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||
|
||||
run 100
|
||||
|
||||
108
examples/USER/pace/log.03Feb2021.pace.product.g++.1
Normal file
108
examples/USER/pace/log.03Feb2021.pace.product.g++.1
Normal file
@ -0,0 +1,108 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple test of fcc Cu with ACE product
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 10 check yes
|
||||
|
||||
variable a equal 3.597
|
||||
lattice fcc $a
|
||||
lattice fcc 3.597
|
||||
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
256 atoms in group Al
|
||||
|
||||
pair_style pace product
|
||||
ACE version: 2021.2.3
|
||||
Product evaluator is used
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
Loading Cu-PBE-core-rep.ace
|
||||
Total number of basis functions
|
||||
Cu: 16 (r=1) 726 (r>1)
|
||||
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||
|
||||
velocity all create 300 8728 loop geom
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
variable delenergy equal c_energy-pe
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.7
|
||||
ghost atom cutoff = 7.7
|
||||
binsize = 3.85, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pace, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
|
||||
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||
0 300 -945.9873 -936.0989 45359.818 0 2.1827873e-11
|
||||
10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11
|
||||
20 228.73618 -943.63789 -936.09844 48903.598 0 -2.910383e-11
|
||||
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
|
||||
40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11
|
||||
50 59.165961 -938.04759 -936.0974 56850.103 0 2.910383e-11
|
||||
60 53.124678 -937.84857 -936.09751 56878.948 0 0
|
||||
70 74.623347 -938.5575 -936.09782 55565.237 0 4.3655746e-11
|
||||
80 109.4762 -939.70663 -936.09815 53665.652 0 2.910383e-11
|
||||
90 142.02657 -940.77975 -936.09837 52001.1 0 0
|
||||
100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11
|
||||
Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms
|
||||
|
||||
Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.468 | 11.468 | 11.468 | 0.0 | 99.96
|
||||
Neigh | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.01
|
||||
Comm | 0.001207 | 0.001207 | 0.001207 | 0.0 | 0.01
|
||||
Output | 0.000876 | 0.000876 | 0.000876 | 0.0 | 0.01
|
||||
Modify | 0.000455 | 0.000455 | 0.000455 | 0.0 | 0.00
|
||||
Other | | 0.000397 | | | 0.00
|
||||
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2201.00 ave 2201 max 2201 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 43118.0 ave 43118 max 43118 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 43118
|
||||
Ave neighs/atom = 168.42969
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:11
|
||||
108
examples/USER/pace/log.03Feb2021.pace.product.g++.4
Normal file
108
examples/USER/pace/log.03Feb2021.pace.product.g++.4
Normal file
@ -0,0 +1,108 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple test of fcc Cu with ACE product
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 10 check yes
|
||||
|
||||
variable a equal 3.597
|
||||
lattice fcc $a
|
||||
lattice fcc 3.597
|
||||
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
256 atoms in group Al
|
||||
|
||||
pair_style pace product
|
||||
ACE version: 2021.2.3
|
||||
Product evaluator is used
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
Loading Cu-PBE-core-rep.ace
|
||||
Total number of basis functions
|
||||
Cu: 16 (r=1) 726 (r>1)
|
||||
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||
|
||||
velocity all create 300 8728 loop geom
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
variable delenergy equal c_energy-pe
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.7
|
||||
ghost atom cutoff = 7.7
|
||||
binsize = 3.85, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pace, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
|
||||
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||
0 300 -945.9873 -936.0989 45359.818 0 -1.4551915e-11
|
||||
10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11
|
||||
20 228.73618 -943.63789 -936.09844 48903.598 0 0
|
||||
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
|
||||
40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11
|
||||
50 59.165961 -938.04759 -936.0974 56850.103 0 -1.4551915e-11
|
||||
60 53.124678 -937.84857 -936.09751 56878.948 0 7.2759576e-12
|
||||
70 74.623347 -938.5575 -936.09782 55565.237 0 0
|
||||
80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11
|
||||
90 142.02657 -940.77975 -936.09837 52001.1 0 -1.4551915e-11
|
||||
100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11
|
||||
Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms
|
||||
|
||||
Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.1375 | 3.3058 | 3.469 | 6.5 | 93.30
|
||||
Neigh | 0.000284 | 0.00031975 | 0.000352 | 0.0 | 0.01
|
||||
Comm | 0.071607 | 0.23492 | 0.40336 | 24.6 | 6.63
|
||||
Output | 0.001189 | 0.0012315 | 0.001347 | 0.2 | 0.03
|
||||
Modify | 0.000311 | 0.00032725 | 0.000351 | 0.0 | 0.01
|
||||
Other | | 0.0005298 | | | 0.01
|
||||
|
||||
Nlocal: 64.0000 ave 71 max 57 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 1373.00 ave 1380 max 1366 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 10779.5 ave 11978 max 9604 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 43118
|
||||
Ave neighs/atom = 168.42969
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.1
Normal file
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.1
Normal file
@ -0,0 +1,108 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple test of fcc Cu with ACE recursive
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 10 check yes
|
||||
|
||||
variable a equal 3.597
|
||||
lattice fcc $a
|
||||
lattice fcc 3.597
|
||||
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
256 atoms in group Al
|
||||
|
||||
pair_style pace recursive
|
||||
ACE version: 2021.2.3
|
||||
Recursive evaluator is used
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
Loading Cu-PBE-core-rep.ace
|
||||
Total number of basis functions
|
||||
Cu: 16 (r=1) 726 (r>1)
|
||||
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||
|
||||
velocity all create 300 8728 loop geom
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
variable delenergy equal c_energy-pe
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.7
|
||||
ghost atom cutoff = 7.7
|
||||
binsize = 3.85, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pace, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
|
||||
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||
0 300 -945.9873 -936.0989 45359.818 0 0
|
||||
10 280.68558 -945.35055 -936.09878 46326.919 0 5.8207661e-11
|
||||
20 228.73618 -943.63789 -936.09844 48903.598 0 1.4551915e-11
|
||||
30 160.53661 -941.38948 -936.09798 52222.083 0 7.2759576e-11
|
||||
40 97.732944 -939.31899 -936.09758 55176.875 0 -5.8207661e-11
|
||||
50 59.165961 -938.04759 -936.0974 56850.103 0 0
|
||||
60 53.124678 -937.84857 -936.09751 56878.948 0 8.7311491e-11
|
||||
70 74.623347 -938.5575 -936.09782 55565.237 0 -1.4551915e-11
|
||||
80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11
|
||||
90 142.02657 -940.77975 -936.09837 52001.1 0 2.910383e-11
|
||||
100 161.73598 -941.42945 -936.09842 51114.997 0 0
|
||||
Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms
|
||||
|
||||
Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.3103 | 9.3103 | 9.3103 | 0.0 | 99.96
|
||||
Neigh | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.01
|
||||
Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.01
|
||||
Output | 0.000827 | 0.000827 | 0.000827 | 0.0 | 0.01
|
||||
Modify | 0.000479 | 0.000479 | 0.000479 | 0.0 | 0.01
|
||||
Other | | 0.000363 | | | 0.00
|
||||
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2201.00 ave 2201 max 2201 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 43118.0 ave 43118 max 43118 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 43118
|
||||
Ave neighs/atom = 168.42969
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:09
|
||||
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.4
Normal file
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.4
Normal file
@ -0,0 +1,108 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple test of fcc Cu with ACE recursive
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 10 check yes
|
||||
|
||||
variable a equal 3.597
|
||||
lattice fcc $a
|
||||
lattice fcc 3.597
|
||||
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
256 atoms in group Al
|
||||
|
||||
pair_style pace recursive
|
||||
ACE version: 2021.2.3
|
||||
Recursive evaluator is used
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
Loading Cu-PBE-core-rep.ace
|
||||
Total number of basis functions
|
||||
Cu: 16 (r=1) 726 (r>1)
|
||||
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||
|
||||
velocity all create 300 8728 loop geom
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
variable delenergy equal c_energy-pe
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.7
|
||||
ghost atom cutoff = 7.7
|
||||
binsize = 3.85, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pace, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
|
||||
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||
0 300 -945.9873 -936.0989 45359.818 0 -5.0931703e-11
|
||||
10 280.68558 -945.35055 -936.09878 46326.919 0 1.4551915e-11
|
||||
20 228.73618 -943.63789 -936.09844 48903.598 0 0
|
||||
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
|
||||
40 97.732944 -939.31899 -936.09758 55176.875 0 0
|
||||
50 59.165961 -938.04759 -936.0974 56850.103 0 -2.910383e-11
|
||||
60 53.124678 -937.84857 -936.09751 56878.948 0 1.4551915e-11
|
||||
70 74.623347 -938.5575 -936.09782 55565.237 0 3.6379788e-11
|
||||
80 109.4762 -939.70663 -936.09815 53665.652 0 -7.2759576e-12
|
||||
90 142.02657 -940.77975 -936.09837 52001.1 0 -2.910383e-11
|
||||
100 161.73598 -941.42945 -936.09842 51114.997 0 7.2759576e-12
|
||||
Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms
|
||||
|
||||
Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5753 | 2.723 | 2.8656 | 6.3 | 93.46
|
||||
Neigh | 0.000308 | 0.000365 | 0.00046 | 0.0 | 0.01
|
||||
Comm | 0.045106 | 0.18792 | 0.33552 | 24.1 | 6.45
|
||||
Output | 0.001213 | 0.001259 | 0.001388 | 0.2 | 0.04
|
||||
Modify | 0.000304 | 0.00033 | 0.00037 | 0.0 | 0.01
|
||||
Other | | 0.0005595 | | | 0.02
|
||||
|
||||
Nlocal: 64.0000 ave 71 max 57 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 1373.00 ave 1380 max 1366 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 10779.5 ave 11978 max 9604 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 43118
|
||||
Ave neighs/atom = 168.42969
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
Reference in New Issue
Block a user