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Merge pull request #3 from akohlmey/pimd_langevin
Update to current develop and some cosmetic changes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,25 @@ | ||
| # FENE beadspring benchmark | ||
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| units lj | ||
| atom_style bond | ||
| units lj | ||
| atom_style bond | ||
| special_bonds fene | ||
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| read_data data.chain | ||
| read_data data.chain | ||
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| neighbor 0.4 bin | ||
| neigh_modify every 1 delay 1 | ||
| neighbor 0.4 bin | ||
| neigh_modify every 1 delay 1 | ||
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| bond_style fene | ||
| bond_coeff 1 30.0 1.5 1.0 1.0 | ||
| bond_coeff 1 30.0 1.5 1.0 1.0 | ||
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| pair_style lj/cut 1.12 | ||
| pair_modify shift yes | ||
| pair_coeff 1 1 1.0 1.0 1.12 | ||
| pair_style lj/cut 1.12 | ||
| pair_modify shift yes | ||
| pair_coeff 1 1 1.0 1.0 1.12 | ||
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| fix 1 all nve | ||
| fix 2 all langevin 1.0 1.0 10.0 904297 | ||
| fix 1 all nve | ||
| fix 2 all langevin 1.0 1.0 10.0 904297 | ||
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| thermo 100 | ||
| timestep 0.012 | ||
| timestep 0.012 | ||
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| run 100 | ||
| run 100 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,32 +1,32 @@ | ||
| # FENE beadspring benchmark | ||
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| variable x index 1 | ||
| variable y index 1 | ||
| variable z index 1 | ||
| variable x index 1 | ||
| variable y index 1 | ||
| variable z index 1 | ||
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| units lj | ||
| atom_style bond | ||
| atom_modify map hash | ||
| units lj | ||
| atom_style bond | ||
| atom_modify map hash | ||
| special_bonds fene | ||
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| read_data data.chain | ||
| read_data data.chain | ||
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| replicate $x $y $z | ||
| replicate $x $y $z | ||
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| neighbor 0.4 bin | ||
| neigh_modify every 1 delay 1 | ||
| neighbor 0.4 bin | ||
| neigh_modify every 1 delay 1 | ||
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| bond_style fene | ||
| bond_coeff 1 30.0 1.5 1.0 1.0 | ||
| bond_coeff 1 30.0 1.5 1.0 1.0 | ||
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| pair_style lj/cut 1.12 | ||
| pair_modify shift yes | ||
| pair_coeff 1 1 1.0 1.0 1.12 | ||
| pair_style lj/cut 1.12 | ||
| pair_modify shift yes | ||
| pair_coeff 1 1 1.0 1.0 1.12 | ||
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| fix 1 all nve | ||
| fix 2 all langevin 1.0 1.0 10.0 904297 | ||
| fix 1 all nve | ||
| fix 2 all langevin 1.0 1.0 10.0 904297 | ||
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| thermo 100 | ||
| timestep 0.012 | ||
| timestep 0.012 | ||
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| run 100 | ||
| run 100 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,33 +1,33 @@ | ||
| # LAMMPS benchmark of granular flow | ||
| # chute flow of 32000 atoms with frozen base at 26 degrees | ||
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| units lj | ||
| atom_style sphere | ||
| boundary p p fs | ||
| newton off | ||
| comm_modify vel yes | ||
| units lj | ||
| atom_style sphere | ||
| boundary p p fs | ||
| newton off | ||
| comm_modify vel yes | ||
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| read_data data.chute | ||
| read_data data.chute | ||
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| pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 | ||
| pair_coeff * * | ||
| pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 | ||
| pair_coeff * * | ||
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| neighbor 0.1 bin | ||
| neigh_modify every 1 delay 0 | ||
| neighbor 0.1 bin | ||
| neigh_modify every 1 delay 0 | ||
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| timestep 0.0001 | ||
| timestep 0.0001 | ||
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| group bottom type 2 | ||
| group active subtract all bottom | ||
| neigh_modify exclude group bottom bottom | ||
| group bottom type 2 | ||
| group active subtract all bottom | ||
| neigh_modify exclude group bottom bottom | ||
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| fix 1 all gravity 1.0 chute 26.0 | ||
| fix 2 bottom freeze | ||
| fix 3 active nve/sphere | ||
| fix 1 all gravity 1.0 chute 26.0 | ||
| fix 2 bottom freeze | ||
| fix 3 active nve/sphere | ||
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| compute 1 all erotate/sphere | ||
| thermo_style custom step atoms ke c_1 vol | ||
| thermo_modify norm no | ||
| thermo 100 | ||
| compute 1 all erotate/sphere | ||
| thermo_style custom step atoms ke c_1 vol | ||
| thermo_modify norm no | ||
| thermo 100 | ||
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| run 100 | ||
| run 100 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,38 +1,38 @@ | ||
| # LAMMPS benchmark of granular flow | ||
| # chute flow of 32000 atoms with frozen base at 26 degrees | ||
|
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| variable x index 1 | ||
| variable y index 1 | ||
| variable x index 1 | ||
| variable y index 1 | ||
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| units lj | ||
| atom_style sphere | ||
| boundary p p fs | ||
| newton off | ||
| comm_modify vel yes | ||
| units lj | ||
| atom_style sphere | ||
| boundary p p fs | ||
| newton off | ||
| comm_modify vel yes | ||
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| read_data data.chute | ||
| read_data data.chute | ||
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| replicate $x $y 1 | ||
| replicate $x $y 1 | ||
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| pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 | ||
| pair_coeff * * | ||
| pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 | ||
| pair_coeff * * | ||
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| neighbor 0.1 bin | ||
| neigh_modify every 1 delay 0 | ||
| neighbor 0.1 bin | ||
| neigh_modify every 1 delay 0 | ||
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| timestep 0.0001 | ||
| timestep 0.0001 | ||
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| group bottom type 2 | ||
| group active subtract all bottom | ||
| neigh_modify exclude group bottom bottom | ||
| group bottom type 2 | ||
| group active subtract all bottom | ||
| neigh_modify exclude group bottom bottom | ||
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| fix 1 all gravity 1.0 chute 26.0 | ||
| fix 2 bottom freeze | ||
| fix 3 active nve/sphere | ||
| fix 1 all gravity 1.0 chute 26.0 | ||
| fix 2 bottom freeze | ||
| fix 3 active nve/sphere | ||
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| compute 1 all erotate/sphere | ||
| thermo_style custom step atoms ke c_1 vol | ||
| thermo_modify norm no | ||
| thermo 100 | ||
| compute 1 all erotate/sphere | ||
| thermo_style custom step atoms ke c_1 vol | ||
| thermo_modify norm no | ||
| thermo 100 | ||
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| run 100 | ||
| run 100 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,32 +1,32 @@ | ||
| # bulk Cu lattice | ||
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| variable x index 1 | ||
| variable y index 1 | ||
| variable z index 1 | ||
| variable x index 1 | ||
| variable y index 1 | ||
| variable z index 1 | ||
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| variable xx equal 20*$x | ||
| variable yy equal 20*$y | ||
| variable zz equal 20*$z | ||
| variable xx equal 20*$x | ||
| variable yy equal 20*$y | ||
| variable zz equal 20*$z | ||
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| units metal | ||
| atom_style atomic | ||
| units metal | ||
| atom_style atomic | ||
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| lattice fcc 3.615 | ||
| region box block 0 ${xx} 0 ${yy} 0 ${zz} | ||
| create_box 1 box | ||
| create_atoms 1 box | ||
| lattice fcc 3.615 | ||
| region box block 0 ${xx} 0 ${yy} 0 ${zz} | ||
| create_box 1 box | ||
| create_atoms 1 box | ||
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| pair_style eam | ||
| pair_coeff 1 1 Cu_u3.eam | ||
| pair_style eam | ||
| pair_coeff 1 1 Cu_u3.eam | ||
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| velocity all create 1600.0 376847 loop geom | ||
| velocity all create 1600.0 376847 loop geom | ||
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| neighbor 1.0 bin | ||
| neighbor 1.0 bin | ||
| neigh_modify every 1 delay 5 check yes | ||
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| fix 1 all nve | ||
| fix 1 all nve | ||
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| timestep 0.005 | ||
| thermo 50 | ||
| timestep 0.005 | ||
| thermo 50 | ||
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| run 100 | ||
| run 100 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,30 @@ | ||
| # 3d Lennard-Jones melt | ||
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| variable x index 1 | ||
| variable y index 1 | ||
| variable z index 1 | ||
| variable x index 1 | ||
| variable y index 1 | ||
| variable z index 1 | ||
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| variable xx equal 20*$x | ||
| variable yy equal 20*$y | ||
| variable zz equal 20*$z | ||
| variable xx equal 20*$x | ||
| variable yy equal 20*$y | ||
| variable zz equal 20*$z | ||
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| units lj | ||
| atom_style atomic | ||
| units lj | ||
| atom_style atomic | ||
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| lattice fcc 0.8442 | ||
| region box block 0 ${xx} 0 ${yy} 0 ${zz} | ||
| create_box 1 box | ||
| create_atoms 1 box | ||
| mass 1 1.0 | ||
| lattice fcc 0.8442 | ||
| region box block 0 ${xx} 0 ${yy} 0 ${zz} | ||
| create_box 1 box | ||
| create_atoms 1 box | ||
| mass 1 1.0 | ||
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| velocity all create 1.44 87287 loop geom | ||
| velocity all create 1.44 87287 loop geom | ||
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| pair_style lj/cut 2.5 | ||
| pair_coeff 1 1 1.0 1.0 2.5 | ||
| pair_style lj/cut 2.5 | ||
| pair_coeff 1 1 1.0 1.0 2.5 | ||
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| neighbor 0.3 bin | ||
| neigh_modify delay 0 every 20 check no | ||
| neighbor 0.3 bin | ||
| neigh_modify delay 0 every 20 check no | ||
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| fix 1 all nve | ||
| fix 1 all nve | ||
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| run 100 | ||
| run 100 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,27 +1,27 @@ | ||
| # Rhodopsin model | ||
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| units real | ||
| neigh_modify delay 5 every 1 | ||
| units real | ||
| neigh_modify delay 5 every 1 | ||
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| atom_style full | ||
| bond_style harmonic | ||
| angle_style charmm | ||
| dihedral_style charmm | ||
| improper_style harmonic | ||
| pair_style lj/charmm/coul/long 8.0 10.0 | ||
| pair_modify mix arithmetic | ||
| kspace_style pppm 1e-4 | ||
| atom_style full | ||
| bond_style harmonic | ||
| angle_style charmm | ||
| dihedral_style charmm | ||
| improper_style harmonic | ||
| pair_style lj/charmm/coul/long 8.0 10.0 | ||
| pair_modify mix arithmetic | ||
| kspace_style pppm 1e-4 | ||
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| read_data data.rhodo | ||
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| fix 1 all shake 0.0001 5 0 m 1.0 a 232 | ||
| fix 2 all npt temp 300.0 300.0 100.0 & | ||
| z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 | ||
| z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 | ||
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| special_bonds charmm | ||
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| thermo 50 | ||
| thermo_style multi | ||
| thermo_style multi | ||
| timestep 2.0 | ||
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| run 100 | ||
| run 100 |
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