From ec1b631e048d8ecef903ae865e1fce3ee905505c Mon Sep 17 00:00:00 2001 From: Andrew Jewett Date: Wed, 4 Dec 2024 13:37:59 -0500 Subject: [PATCH] fixed issue #100 (corrected example comments describing pressure conditions) --- examples/all_atom/force_field_AMBER/benzene/run.in.npt | 4 ++-- .../all_atom/force_field_AMBER/ethylene+benzene/run.in.npt | 4 ++-- examples/all_atom/force_field_AMBER/hexadecane/run.in.npt | 4 ++-- .../force_field_OPLSAA/benzene+benzoic_acid/run.in.npt | 4 ++-- .../all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt | 4 ++-- .../force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt | 2 +- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/examples/all_atom/force_field_AMBER/benzene/run.in.npt b/examples/all_atom/force_field_AMBER/benzene/run.in.npt index c789573a..fa1d8418 100644 --- a/examples/all_atom/force_field_AMBER/benzene/run.in.npt +++ b/examples/all_atom/force_field_AMBER/benzene/run.in.npt @@ -53,7 +53,7 @@ print " (In case there are any. I'm not certain there are." print " Later we will restore ordinary pressure.)" print "---------------------------------------------------------------------------" fix fxlan all langevin 298.0 298.0 5000 123456 # temp: 298 K -fix fxnph all nph iso 500.0 500.0 1000.0 # pressure: 500 barr +fix fxnph all nph iso 500.0 500.0 1000.0 # pressure: 500 atm run 80000 unfix fxlan @@ -64,7 +64,7 @@ unfix fxnph print "---------------------------------------------------------------------------" print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" print "---------------------------------------------------------------------------" -# temperature: 298 K, pressure: 1 barr +# temperature: 298 K, pressure: 1 atm fix fxnpt all npt temp 298.0 298.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 #thermo_modify flush yes diff --git a/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt b/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt index 92962f60..5bf13fe3 100644 --- a/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt +++ b/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt @@ -39,7 +39,7 @@ print "------------------------------------------------------------------------- velocity all create 300.0 12345 fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K -fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr +fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 atm thermo 100 run 2000 unfix fxlan @@ -49,7 +49,7 @@ print "------------------------------------------------------------------------- print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" print "---------------------------------------------------------------------------" dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 50 barr +# temperature: 300 K, pressure: 50 atm fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 thermo 100 #thermo_modify flush yes diff --git a/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt b/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt index 85a33e81..fbb9cbe2 100644 --- a/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt +++ b/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt @@ -85,8 +85,8 @@ unfix fxnvt # I did this to enable the molecules to move freely and reorient themselves. # After doing that, we should run the simulation under NPT conditions to # allow the simulation box to contract to it's natural size. We do that here: -# We begin the simulation at 100 barr (a relatively low pressure), and -# slowly decrease it to 1 barr, maintianing the temperature at 300K. +# We begin the simulation at 100 atm (a relatively low pressure), and +# slowly decrease it to 1 atm, maintianing the temperature at 300K. dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz fix fxnpt all npt temp 900.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 diff --git a/examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/run.in.npt b/examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/run.in.npt index d221d984..53323e84 100644 --- a/examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/run.in.npt +++ b/examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/run.in.npt @@ -43,7 +43,7 @@ velocity all create 300.0 12345 # Run a short simulation using a Langevin thermostat (for improved stability). fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K -fix fxnph all nph iso 150.0 150.0 1000.0 # pressure: 150 barr +fix fxnph all nph iso 150.0 150.0 1000.0 # pressure: 150 atm run 2000 unfix fxlan unfix fxnph @@ -52,7 +52,7 @@ print "------------------------------------------------------------------------- print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" print "---------------------------------------------------------------------------" dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 150 barr +# temperature: 300 K, pressure: 150 atm fix fxnpt all npt temp 300.0 300.0 100.0 iso 150.0 150.0 1000.0 drag 1.0 thermo 100 #thermo_modify flush yes diff --git a/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt b/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt index d221d984..53323e84 100644 --- a/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt +++ b/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt @@ -43,7 +43,7 @@ velocity all create 300.0 12345 # Run a short simulation using a Langevin thermostat (for improved stability). fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K -fix fxnph all nph iso 150.0 150.0 1000.0 # pressure: 150 barr +fix fxnph all nph iso 150.0 150.0 1000.0 # pressure: 150 atm run 2000 unfix fxlan unfix fxnph @@ -52,7 +52,7 @@ print "------------------------------------------------------------------------- print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" print "---------------------------------------------------------------------------" dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 150 barr +# temperature: 300 K, pressure: 150 atm fix fxnpt all npt temp 300.0 300.0 100.0 iso 150.0 150.0 1000.0 drag 1.0 thermo 100 #thermo_modify flush yes diff --git a/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt b/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt index 3a2d12dd..367661ec 100644 --- a/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt +++ b/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt @@ -37,7 +37,7 @@ print "----------------------------------------------------------------" print "--- Run a simulation using a Nose-Hoover Thermostat/Barostat ---" print "----------------------------------------------------------------" dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 150 barr +# temperature: 300 K, pressure: 150 atm fix fxnpt all npt temp 300.0 300.0 100.0 iso 150.0 150.0 1000.0 drag 1.0 thermo 100 #thermo_modify flush yes