fixed issue #100 (corrected example comments describing pressure cond…

…itions)

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
 

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

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

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

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

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