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sirmarcelsirmarcel
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‎examples/o3-averaging/data/in-mol.lmp

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units electron
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atom_style full
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pair_style lj/cut/tip4p/cut 1 2 1 1 0.278072379 17.001
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# high-pppm precision and shift to get meaningful fd estimates
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# kspace_style none
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# kspace_style pppm/tip4p 1e-5
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pair_modify shift yes
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bond_style class2
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angle_style harmonic
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read_data water_1_data.lmp
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pair_coeff * * 0 0
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pair_coeff 1 1 0.000295147 5.96946
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neighbor 2.0 bin
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timestep 0.00025
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#velocity all create 298.0 2345187
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#thermo_style multi
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#thermo 1
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#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1
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#fix 1 all nve
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fix 1 all ipi h2o-lammps 32342 unix
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#dump 1 all xyz 25 dump.xyz
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run 100000000
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‎examples/o3-averaging/data/init-mol.xyz

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3
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Lattice="100.0 0.0 0.0 0.0 100.0 0.0 0.0 0.0 100.0" Properties=species:S:1:pos:R:3:momenta:R:3 ipi_comment="Step: 200000 Bead: 0 positions{angstrom} cell{angstrom}" pbc="T T T"
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O -2.89770838 6.76492149 25.78733892 0.41094839 -0.09429088 0.29861888
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H -3.22693259 6.92327461 24.89600383 -0.31547195 0.04597911 -0.02131858
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H -3.73951469 6.82619967 26.21403556 -0.09547645 0.04831177 -0.27730030

‎examples/o3-averaging/data/input-mol-grid.xml

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<!-- safe_stride is the frequency at which i-PI makes internal snapshots for restarting -->
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<simulation verbosity='medium' threading='false' safe_stride='10'>
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<ffsocket name='lmpserial' mode='unix' pbc='false'>
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<address>h2o-lammps</address> <latency> 1e-4 </latency>
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</ffsocket>
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<ffrotations name='driver-noo3' mode='unix' pbc='false'>
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<address>h2o-noo3</address>
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<grid_order> 3 </grid_order>
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<grid_mode> legendre </grid_mode>
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<inversion> True </inversion>
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</ffrotations>
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<total_steps>10000</total_steps>
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<output prefix='nve-mol'>
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<trajectory stride='20' filename='pos' format='xyz'> positions </trajectory>
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<properties stride='20'> [ step, time, conserved, temperature{kelvin}, kinetic_md, potential, pressure_md ] </properties>
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</output>
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<prng>
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<seed>32123</seed>
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</prng>
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<system>
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<forces>
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<force forcefield='lmpserial'></force>
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<force forcefield='driver-noo3' weight="1.0"/>
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</forces>
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<initialize nbeads='1'>
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<file mode='ase'> init-mol.xyz </file>
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</initialize>
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<ensemble>
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<temperature units='kelvin'> 300 </temperature>
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</ensemble>
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<motion mode='dynamics'>
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<fixcom> True </fixcom>
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<dynamics mode='nve'>
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<timestep units='femtosecond'> 0.5 </timestep>
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</dynamics>
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</motion>
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</system>
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</simulation>

‎examples/o3-averaging/data/input-mol-noo3.xml

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<!-- safe_stride is the frequency at which i-PI makes internal snapshots for restarting -->
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<simulation verbosity='medium' threading='false' safe_stride='10'>
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<ffsocket name='lmpserial' mode='unix' pbc='false'>
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<address>h2o-lammps</address> <latency> 1e-4 </latency>
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</ffsocket>
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<ffsocket name='driver-noo3' mode='unix' pbc='false'>
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<address>h2o-noo3</address>
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</ffsocket>
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<total_steps>10000</total_steps>
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<output prefix='nve-mol'>
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<trajectory stride='20' filename='pos' format='xyz'> positions </trajectory>
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<properties stride='20'> [ step, time, conserved, temperature{kelvin}, kinetic_md, potential, pressure_md ] </properties>
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</output>
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<prng>
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<seed>32123</seed>
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</prng>
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<system>
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<forces>
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<force forcefield='lmpserial'></force>
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<force forcefield='driver-noo3' weight="1.0"/>
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</forces>
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<initialize nbeads='1'>
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<file mode='ase'> init-mol.xyz </file>
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</initialize>
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<ensemble>
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<temperature units='kelvin'> 300 </temperature>
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</ensemble>
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<motion mode='dynamics'>
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<fixcom> True </fixcom>
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<dynamics mode='nve'>
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<timestep units='femtosecond'> 0.5 </timestep>
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</dynamics>
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</motion>
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</system>
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</simulation>

‎examples/o3-averaging/data/replay-noo3.xml

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<simulation verbosity='medium' safe_stride='100'>
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<output prefix='water-noo3'>
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<properties filename='out' stride='1'>
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[ step, time{picosecond}, conserved, potential, kinetic_cv,
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scaledcoords(fd_delta=5e-3) ]
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</properties>
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</output>
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<ffsocket name='lmpserial' mode='unix' pbc='false'>
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<address>h2o-lammps</address> <latency> 1e-4 </latency>
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</ffsocket>
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<ffrotations name='noo3' mode='unix' pbc='false'>
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<address>h2o-noo3</address> <latency> 1e-4 </latency>
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</ffrotations>
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<system>
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<initialize nbeads='1'>
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<file mode='ase' units='angstrom'> init-mol.xyz </file>
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</initialize>
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<forces>
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<force forcefield='lmpserial'/>
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<force forcefield='noo3'/>
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</forces>
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<motion mode='replay'>
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<file mode='ase'> replay.xyz </file>
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</motion>
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</system>
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</simulation>

‎examples/o3-averaging/data/water_1_data.lmp

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LAMMPS Description
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3 atoms
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2 bonds
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1 angles
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2 atom types
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1 bond types
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1 angle types
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-19 19.38859 xlo xhi
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-10 19.38859 ylo yhi
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-19 19.38859 zlo zhi
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Masses
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1 15.9994
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2 1.0080
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Bond Coeffs
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1 1.78 0.2708585 -0.327738785 0.231328959
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Angle Coeffs
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1 0.0700 107.400000
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Atoms
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1 1 1 -1.1128 7.098 8.901 17.941
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2 1 2 0.5564 8.700 8.073 18.276
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3 1 2 0.5564 7.555 10.053 16.607
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Bonds
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1 1 1 2
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2 1 1 3
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Angles
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1 1 2 1 3

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