diff --git a/src/test/scala/eu/nomad_lab/parsers/LammpsParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/LammpsParserSpec.scala index 85cf1d4218d4114ccf01d9f25ee3071568379788..3833f7b516f0085a0456a1bad01697faf0b0ff5e 100644 --- a/src/test/scala/eu/nomad_lab/parsers/LammpsParserSpec.scala +++ b/src/test/scala/eu/nomad_lab/parsers/LammpsParserSpec.scala @@ -5,10 +5,10 @@ import org.specs2.mutable.Specification object LammpsParserSpec extends Specification { "LammpsParserTest" >> { "test with json-events" >> { - ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/mainlog.64xmethane-nvt-thermo_style_custom", "json-events") must_== ParseResult.ParseSuccess + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/log.64xmethane-nvt-thermo_style_custom", "json-events") must_== ParseResult.ParseSuccess } "test with json" >> { - ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/mainlog.64xmethane-nvt-thermo_style_custom", "json") must_== ParseResult.ParseSuccess + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/log.64xmethane-nvt-thermo_style_custom", "json") must_== ParseResult.ParseSuccess } } } @@ -16,10 +16,10 @@ object LammpsParserSpec extends Specification { object LammpsParserSpec1 extends Specification { "LammpsParserTest1" >> { "test with json-events 1" >> { - ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/mainlog.64xmethane-nvt-thermo_style_one", "json-events") must_== ParseResult.ParseSuccess + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/log.64xmethane-nvt-thermo_style_one", "json-events") must_== ParseResult.ParseSuccess } "test with json 1" >> { - ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/mainlog.64xmethane-nvt-thermo_style_one", "json") must_== ParseResult.ParseSuccess + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/log.64xmethane-nvt-thermo_style_one", "json") must_== ParseResult.ParseSuccess } } } @@ -27,10 +27,10 @@ object LammpsParserSpec1 extends Specification { object LammpsParserSpec2 extends Specification { "LammpsParserTest2" >> { "test with json-events 2" >> { - ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/mainlog.64xmethane-nvt-thermo_style_multi", "json-events") must_== ParseResult.ParseSuccess + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/log.64xmethane-nvt-thermo_style_multi", "json-events") must_== ParseResult.ParseSuccess } "test with json 2" >> { - ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/mainlog.64xmethane-nvt-thermo_style_multi", "json") must_== ParseResult.ParseSuccess + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane/log.64xmethane-nvt-thermo_style_multi", "json") must_== ParseResult.ParseSuccess } } } @@ -46,36 +46,36 @@ object LammpsParserSpec2 extends Specification { // } // } -// object LammpsParserSpec4 extends Specification { -// "LammpsParserTest4" >> { -// "test with json-events 4" >> { -// ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/hexane_cyclohexane/log.hexane_cyclohexane_nvt", "json-events") must_== ParseResult.ParseSuccess -// } -// "test with json 4" >> { -// ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/hexane_cyclohexane/log.hexane_cyclohexane_nvt", "json") must_== ParseResult.ParseSuccess -// } -// } -// } +object LammpsParserSpec4 extends Specification { + "LammpsParserTest4" >> { + "test with json-events 4" >> { + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/hexane_cyclohexane/log.hexane_cyclohexane_nvt", "json-events") must_== ParseResult.ParseSuccess + } + "test with json 4" >> { + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/hexane_cyclohexane/log.hexane_cyclohexane_nvt", "json") must_== ParseResult.ParseSuccess + } + } +} -// object LammpsParserSpec5 extends Specification { -// "LammpsParserTest5" >> { -// "test with json-events 5" >> { -// ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom", "json-events") must_== ParseResult.ParseSuccess -// } -// "test with json 5" >> { -// ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom", "json") must_== ParseResult.ParseSuccess -// } -// } -// } +object LammpsParserSpec5 extends Specification { + "LammpsParserTest5" >> { + "test with json-events 5" >> { + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom", "json-events") must_== ParseResult.ParseSuccess + } + "test with json 5" >> { + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom", "json") must_== ParseResult.ParseSuccess + } + } +} -// object LammpsParserSpec6 extends Specification { -// "LammpsParserTest6" >> { -// "test with json-events 6" >> { -// ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom", "json-events") must_== ParseResult.ParseSuccess -// } -// "test with json 6" >> { -// ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom", "json") must_== ParseResult.ParseSuccess -// } -// } -// } +object LammpsParserSpec6 extends Specification { + "LammpsParserTest6" >> { + "test with json-events 6" >> { + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom", "json-events") must_== ParseResult.ParseSuccess + } + "test with json 6" >> { + ParserRun.parse(LammpsParser, "parsers/lammps/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom", "json") must_== ParseResult.ParseSuccess + } + } +} diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_atom_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_atom_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..dfe14f0efe75f7b92851f91e4e58ce3811f2f8e6 --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_atom_thermo_style_custom @@ -0,0 +1,74 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + + + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +# dump 1 all xtc 400 64xmethane-nvt.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_atom_unscaled_image_flags_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_atom_unscaled_image_flags_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..f8bb20f52a16d133358676c0e7943dd0685e3c00 --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_atom_unscaled_image_flags_thermo_style_custom @@ -0,0 +1,71 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +# dump 1 all xtc 400 64xmethane-nvt.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +dump 1 all atom 400 64xmethane-nvt_unscaled_image_flags.atom +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +dump_modify 1 image yes scale no + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..24e1fc9bfc7affe42c35654d8cc0a8ed42fde773 --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_thermo_style_custom @@ -0,0 +1,71 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +dump 1 all dcd 400 64xmethane-nvt.dcd +# dump 1 all xtc 400 64xmethane-nvt.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_unwrapped_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_unwrapped_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..4626fb22c99094d8e63b15538b290fd9e26f606d --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_dcd_unwrapped_thermo_style_custom @@ -0,0 +1,73 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +dump 1 all dcd 400 64xmethane-nvt_unwrapped.dcd +# dump 1 all xtc 400 64xmethane-nvt.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no +dump_modify 1 unwrap yes + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_lammpstrj_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_lammpstrj_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..f14afa7c378d035a3bcafdabadb145f3378cbc9d --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_lammpstrj_thermo_style_custom @@ -0,0 +1,71 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +# dump 1 all xtc 400 64xmethane-nvt.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..2562336277d7e0813a8969c5398c64f3a3756421 --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_thermo_style_custom @@ -0,0 +1,72 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +dump 1 all xtc 400 64xmethane-nvt.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_unwrapped_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_unwrapped_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..41d5c52310dafdc24a57d0a38ad603decd304a12 --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_xtc_unwrapped_thermo_style_custom @@ -0,0 +1,74 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 3 by 2 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +#dihedral_style opls +pair_modify mix geometric tail yes + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +# dump 1 all dcd 400 64xmethane-nvt.dcd_unwrapped +# dump 1 all xtc 400 64xmethane-nvt.xtc +dump 1 all xtc 400 64xmethane-nvt_unwrapped.xtc +# dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no +dump_modify 1 unwrap yes + +# output log +log log.64xmethane-nvt-thermo_style_custom diff --git a/test/examples/methane_MD_traj/log.methane_nvt_traj_xyz_thermo_style_custom b/test/examples/methane_MD_traj/log.methane_nvt_traj_xyz_thermo_style_custom new file mode 100644 index 0000000000000000000000000000000000000000..dc35e1db816ebc7d0311c5febbfc296d3102b8f4 --- /dev/null +++ b/test/examples/methane_MD_traj/log.methane_nvt_traj_xyz_thermo_style_custom @@ -0,0 +1,74 @@ +LAMMPS (14 May 2016) +# input script for topotools tutorial step 2a +units real +boundary p p p +atom_style full + + +# interaction styles +pair_style lj/cut/coul/cut 12.0 +bond_style harmonic +angle_style harmonic + +read_data data.64xmethane_from_restart + orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 256 bonds + reading angles ... + 384 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + + +#dihedral_style opls +pair_modify mix geometric tail yes + + +# OPLS considers 1-4 interactions with 50%. +special_bonds lj/coul 0.0 0.0 0.5 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# force field parameters +pair_coeff 1 1 0.066 3.5 # CT +pair_coeff 2 2 0.03 2.5 # HC +# the remaining parameters are inferred from mixing. +bond_coeff 1 340.0 1.09 # CT-HC +angle_coeff 1 33.0 107.8 # HC-CT-HC + +# equilibration. real methane freezes at 91K and boils at 112K +# so we hope the force field has it as a liquid at 100K. +timestep 0.25 +reset_timestep 0 +neighbor 1.5 bin +neigh_modify every 10 delay 20 check yes +thermo 400 +thermo_style custom step temp pe ke press vol density + +fix 2 all nvt temp 100.0 100.0 100.0 + +# equilibration trajectory + +# dump 1 all dcd 400 64xmethane-nvt.dcd +# dump 1 all xtc 400 64xmethane-nvt.xtc +dump 1 all xyz 400 64xmethane-nvt.xyz +# dump 1 all atom 400 64xmethane-nvt.atom +# dump 1 all atom 400 64xmethane-nvt.atom_unscaled_image_flags +# dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z vx vy vz fx fy fz ix iy iz +# dump_modify 1 image yes scale no + +# output log +log log.64xmethane-nvt-thermo_style_custom