git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15130 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/USER/dpd/README

@@ -1,8 +1,10 @@
 This directory contains input files for DPD simulations under
-isothermal, isoenergetic, isobaric and isoenthalpic conditions.  All
+isothermal, isoenergetic, isobaric and isoenthalpic conditions.  In
-the DPD scenarios use the Shardlow splitting algorithm to integrate
+addition, there is also an example for a reaction DPD simulation under
-the equations of motion.  The compute dpd command is used in the
+isoenergetic conditions.  All the DPD scenarios use the Shardlow
-isoenergetic and isenthalpic case to demonstrate how one can access
+splitting algorithm to integrate the equations of motion.  The compute
-the particle internal energies.
+dpd command is used in the isoenergetic and isenthalpic case to
+demonstrate how one can access the particle internal energies.
+
 
 

examples/USER/dpd/dpdrx-shardlow/in.dpdrx

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+# Example for running DPD-RX
+
+log             log.dpdrx
+boundary        p p p
+units           metal  # ev, ps
+atom_style      dpd
+atom_modify     map array
+##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
+fix             4 all rx kinetics.dpdrx none lammps_rk4 1
+#fix             4 all rx kinetics_null.dpdrx none lammps_rk4
+
+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
+region          box block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_box      2 box
+region          atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_atoms    1 region atoms
+
+comm_modify     mode single vel yes
+mass            * 222.12
+
+#Set concentrations
+set atom * d_rdx 1.00
+set atom * d_h2 0.0
+set atom * d_no2 0.0
+set atom * d_n2 0.0
+set atom * d_hcn 0.0
+set atom * d_no 0.0
+set atom * d_h2o 0.0
+set atom * d_co 0.0
+set atom * d_co2 0.0
+
+#Set the internal temperature of the particles
+set             atom * dpd/theta 2065.00
+
+#Set the kinetic temperature of the particles
+velocity	all create 2065.0 875661 dist gaussian
+
+timestep        0.001
+
+pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
+pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+
+fix             1 all shardlow
+fix             2 all nve
+fix             3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
+#fix             4 all rx lammps_rk4 kinetics.dpdrx
+
+compute         dpdU all dpd
+compute         dpdUatom all dpd/atom
+compute         crdx all property/atom d_rdx
+
+variable        totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
+
+thermo          1
+thermo_style    custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
+thermo_modify   format float %15.8f flush yes
+
+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
+dump_modify     2 sort id
+
+restart         10 restart.dpdrx
+
+write_data      data.dpdrx.initial
+run 10
+write_data      data.dpdrx.final

examples/USER/dpd/dpdrx-shardlow/in.dpdrx.old

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+# Example for running DPD-RX
+
+log             log.dpdrx
+boundary        p p p
+units           metal  # ev, ps
+atom_style      dpd
+atom_modify     map array
+#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
+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
+fix             4 all rx kinetics.dpdrx none lammps_rk4
+#fix             4 all rx kinetics_null.dpdrx none lammps_rk4
+#fix             4 all rx lammps_rk4 kinetics.dpdrx
+
+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
+region          box block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_box      2 box
+region          atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_atoms    1 region atoms
+
+comm_modify     mode single vel yes
+mass            * 222.12
+
+#Set concentrations
+set atom * d_rdx 1.00
+set atom * d_h2 0.0
+set atom * d_no2 0.0
+set atom * d_n2 0.0
+set atom * d_hcn 0.0
+set atom * d_no 0.0
+set atom * d_h2o 0.0
+set atom * d_co 0.0
+set atom * d_co2 0.0
+
+#Set the internal temperature of the particles
+set             atom * dpd/theta 2065.00
+
+#Set the kinetic temperature of the particles
+velocity	all create 2065.0 875661 dist gaussian
+
+timestep        0.001
+
+pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
+pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+
+fix             1 all shardlow
+fix             2 all nve
+fix             3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
+#fix             4 all rx lammps_rk4 kinetics.dpdrx
+
+compute         dpdU all dpd
+compute         dpdUatom all dpd/atom
+compute         crdx all property/atom d_rdx
+
+variable        totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
+
+thermo          1
+thermo_style    custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
+thermo_modify   format float %15.8f flush yes
+
+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
+dump_modify     2 sort id
+
+restart         10 restart.dpdrx
+
+write_data      data.dpdrx.initial
+run 10
+write_data      data.dpdrx.final

examples/USER/dpd/dpdrx-shardlow/kinetics.dpdrx

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+# reaction equations and parameters
+# multiple entries can be added to this file
+# these entries are in LAMMPS "metal" units:
+#   Arr = 1/picosec or Angstroms^3/mol/picosec; Ern = eV
+
+# format of a single entry (one or more lines):
+#   rxn equation, Arn, Ern
+
+1.0 rdx           = 3.0 hcn + 1.5 no2 + 1.5 no + 1.5 h2o  2.51000000000000E+04 0.0 1.912325921964536
+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
+1.0 hcn + 1.0  no = 1.0  co + 1.0 n2  + 0.5 h2            4.98162056E+00 0.0 1.517718985686140
+1.0  no + 1.0  co = 0.5  n2 + 1.0 co2                     1.66054018667494E+06 0.0 6.938245245

examples/USER/dpd/dpdrx-shardlow/kinetics_null.dpdrx

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+# reaction equations and parameters
+# multiple entries can be added to this file
+# these entries are in LAMMPS "metal" units:
+#   Arr = 1/picosec or Angstroms^3/mol/picosec; Ern = eV
+
+# format of a single entry (one or more lines):
+#   rxn equation, Arn, Ern
+
+1.0 rdx           = 3.0 hcn + 1.5 no2 + 1.5 no + 1.5 h2o  0.0 0.0 1.912325921964536
+1.0 hcn + 1.0 no2 = 1.0  no + 0.5 n2  + 0.5 h2 + 1.0 co   0.0 0.0 1.344265387322009
+1.0 hcn + 1.0  no = 1.0  co + 1.0 n2  + 0.5 h2            0.0 0.0 1.517718985686140
+1.0  no + 1.0  co = 0.5  n2 + 1.0 co2                     0.0 0.0 6.938245245

examples/USER/dpd/dpdrx-shardlow/params.exp6

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+# rx parameters for various molecules
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units:
+#   alpha = unitless; epsilon = eV; rho = Angstroms; 
+
+# format of a single entry (one or more lines):
+#   species, exp6, alpha, epsilon, rm
+
+hcn     exp6  13.57  0.030862657941745  5.3725
+no2     exp6  13.57  0.029126283357001  4.2744
+no      exp6  13.10  0.013090454747817  3.7142
+h2o     exp6  11.01  0.022473771300313  3.5348
+co      exp6  13.24  0.0086353397713660428  4.1759
+co2     exp6  14.09  0.019672305322873507  4.1757
+h2      exp6  11.23  0.002618780329051 3.4925
+n2      exp6  12.97  0.008635339808299 4.1778

examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx

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+# rx heats of formation for various molecules
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# the entries are in LAMMPS "metal" units (eV)
+# Be sure the units are consistent with your input file
+
+# format of a single entry (one or more lines):
+#   species  DeltaHformation
+
+rdx     1.989907438211819
+h2      0.000000000000000
+no2     0.343004076201018
+n2      0.000000000000000
+hcn     1.400635733970104
+no      0.935781955892458
+h2o    -2.506184777415379
+co     -1.145533746031845
+co2    -4.078501848437456

examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx.new

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+# rx heats of formation for various molecules
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# the entries are in LAMMPS "metal" units (eV)
+# Be sure the units are consistent with your input file
+
+# format of a single entry (one or more lines):
+#   species  DeltaHformation
+
+rdx     1.989907438211819
+hcn     1.400635733970104
+no2     0.343004076201018
+no      0.935781955892458
+h2o    -2.506184777415379
+n2      0.000000000000000
+h2      0.000000000000000
+co     -1.145533746031845
+co2    -4.078501848437456