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This directory contains input files for DPD simulations under
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isothermal, isoenergetic, isobaric and isoenthalpic conditions. All
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the DPD scenarios use the Shardlow splitting algorithm to integrate
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the equations of motion. The compute dpd command is used in the
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isoenergetic and isenthalpic case to demonstrate how one can access
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the particle internal energies.
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isothermal, isoenergetic, isobaric and isoenthalpic conditions. In
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addition, there is also an example for a reaction DPD simulation under
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isoenergetic conditions. All the DPD scenarios use the Shardlow
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splitting algorithm to integrate the equations of motion. The compute
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dpd command is used in the isoenergetic and isenthalpic case to
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demonstrate how one can access the particle internal energies.
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# Example for running DPD-RX
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log log.dpdrx
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boundary p p p
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units metal # ev, ps
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atom_style dpd
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atom_modify map array
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##fix Concentrations all property/atom d_rdx d_h2 d_no2 d_n2 d_hcn d_no d_h2o d_co d_co2 ghost yes
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fix 4 all rx kinetics.dpdrx none lammps_rk4 1
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#fix 4 all rx kinetics_null.dpdrx none lammps_rk4
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lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
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region box block 0 6.0 0 6.0 0.0 6.0 units lattice
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create_box 2 box
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region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
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create_atoms 1 region atoms
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comm_modify mode single vel yes
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mass * 222.12
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#Set concentrations
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set atom * d_rdx 1.00
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set atom * d_h2 0.0
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set atom * d_no2 0.0
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set atom * d_n2 0.0
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set atom * d_hcn 0.0
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set atom * d_no 0.0
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set atom * d_h2o 0.0
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set atom * d_co 0.0
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set atom * d_co2 0.0
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#Set the internal temperature of the particles
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set atom * dpd/theta 2065.00
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#Set the kinetic temperature of the particles
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velocity all create 2065.0 875661 dist gaussian
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timestep 0.001
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pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
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pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
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pair_coeff * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
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fix 1 all shardlow
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fix 2 all nve
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fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
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#fix 4 all rx lammps_rk4 kinetics.dpdrx
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compute dpdU all dpd
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compute dpdUatom all dpd/atom
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compute crdx all property/atom d_rdx
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variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
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thermo 1
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thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
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thermo_modify format float %15.8f flush yes
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dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
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dump_modify 2 sort id
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restart 10 restart.dpdrx
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write_data data.dpdrx.initial
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run 10
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write_data data.dpdrx.final
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# Example for running DPD-RX
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log log.dpdrx
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boundary p p p
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units metal # ev, ps
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atom_style dpd
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atom_modify map array
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#fix Concentrations all property/atom rx_rdx rx_hcn rx_no2 rx_no rx_h2o rx_n2 rx_h2 rx_co rx_co2 ghost yes
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fix Concentrations all property/atom rx_rdx rx_h2 rx_no2 rx_n2 rx_hcn rx_no rx_h2o rx_co rx_co2 ghost yes
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fix 4 all rx kinetics.dpdrx none lammps_rk4
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#fix 4 all rx kinetics_null.dpdrx none lammps_rk4
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#fix 4 all rx lammps_rk4 kinetics.dpdrx
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lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
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region box block 0 6.0 0 6.0 0.0 6.0 units lattice
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create_box 2 box
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region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
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create_atoms 1 region atoms
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comm_modify mode single vel yes
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mass * 222.12
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#Set concentrations
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set atom * d_rdx 1.00
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set atom * d_h2 0.0
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set atom * d_no2 0.0
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set atom * d_n2 0.0
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set atom * d_hcn 0.0
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set atom * d_no 0.0
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set atom * d_h2o 0.0
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set atom * d_co 0.0
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set atom * d_co2 0.0
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#Set the internal temperature of the particles
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set atom * dpd/theta 2065.00
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#Set the kinetic temperature of the particles
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velocity all create 2065.0 875661 dist gaussian
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timestep 0.001
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pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
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pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
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pair_coeff * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
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fix 1 all shardlow
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fix 2 all nve
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fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
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#fix 4 all rx lammps_rk4 kinetics.dpdrx
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compute dpdU all dpd
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compute dpdUatom all dpd/atom
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compute crdx all property/atom d_rdx
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variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
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thermo 1
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thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
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thermo_modify format float %15.8f flush yes
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dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
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dump_modify 2 sort id
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restart 10 restart.dpdrx
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write_data data.dpdrx.initial
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run 10
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write_data data.dpdrx.final
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# reaction equations and parameters
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# multiple entries can be added to this file
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# these entries are in LAMMPS "metal" units:
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# Arr = 1/picosec or Angstroms^3/mol/picosec; Ern = eV
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# format of a single entry (one or more lines):
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# rxn equation, Arn, Ern
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1.0 rdx = 3.0 hcn + 1.5 no2 + 1.5 no + 1.5 h2o 2.51000000000000E+04 0.0 1.912325921964536
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1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49081028001241E+01 0.0 1.344265387322009
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1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 4.98162056E+00 0.0 1.517718985686140
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1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66054018667494E+06 0.0 6.938245245
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# reaction equations and parameters
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# multiple entries can be added to this file
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# these entries are in LAMMPS "metal" units:
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# Arr = 1/picosec or Angstroms^3/mol/picosec; Ern = eV
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# format of a single entry (one or more lines):
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# rxn equation, Arn, Ern
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1.0 rdx = 3.0 hcn + 1.5 no2 + 1.5 no + 1.5 h2o 0.0 0.0 1.912325921964536
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1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 0.0 0.0 1.344265387322009
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1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 0.0 0.0 1.517718985686140
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1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 0.0 0.0 6.938245245
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# rx parameters for various molecules
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# alpha = unitless; epsilon = eV; rho = Angstroms;
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# format of a single entry (one or more lines):
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# species, exp6, alpha, epsilon, rm
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hcn exp6 13.57 0.030862657941745 5.3725
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no2 exp6 13.57 0.029126283357001 4.2744
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no exp6 13.10 0.013090454747817 3.7142
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h2o exp6 11.01 0.022473771300313 3.5348
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co exp6 13.24 0.0086353397713660428 4.1759
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co2 exp6 14.09 0.019672305322873507 4.1757
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h2 exp6 11.23 0.002618780329051 3.4925
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n2 exp6 12.97 0.008635339808299 4.1778
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File diff suppressed because it is too large
Load Diff
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# rx heats of formation for various molecules
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# the entries are in LAMMPS "metal" units (eV)
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# Be sure the units are consistent with your input file
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# format of a single entry (one or more lines):
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# species DeltaHformation
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rdx 1.989907438211819
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h2 0.000000000000000
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no2 0.343004076201018
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n2 0.000000000000000
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hcn 1.400635733970104
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no 0.935781955892458
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h2o -2.506184777415379
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co -1.145533746031845
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co2 -4.078501848437456
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# rx heats of formation for various molecules
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# the entries are in LAMMPS "metal" units (eV)
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# Be sure the units are consistent with your input file
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# format of a single entry (one or more lines):
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# species DeltaHformation
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rdx 1.989907438211819
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hcn 1.400635733970104
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no2 0.343004076201018
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no 0.935781955892458
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h2o -2.506184777415379
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n2 0.000000000000000
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h2 0.000000000000000
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co -1.145533746031845
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co2 -4.078501848437456
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