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add harmonic/cut to python example folder. small tweaks to docs and examples

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Axel Kohlmeyer
2022-03-18 17:58:30 -04:00
parent 6c6a6b7c64
commit a7fce6dc39
18 changed files with 1354 additions and 213 deletions
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28
examples/python/in.pair_python_long
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@ -1,25 +1,25 @@
units real
atom_style full
units real
atom_style full
read_data data.spce
read_data data.spce
pair_style python 12.0
pair_coeff * * py_pot.LJCutSPCE OW HW
pair_style python 12.0
pair_coeff * * py_pot.LJCutSPCE OW HW
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 1.0
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
@ -27,7 +27,7 @@ pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
# switch to tabulated potential with long-range coulomb as overlay
pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 1 table spce.table OW-OW